The information in this publication is provided for ...turroserver.chem.columbia.edu/group/instrument/Nexus870.pdfThe information in this publication is provided for reference

The information in this publication is provided for reference only. All information contained inthis publication is believed to be correct and complete. Nicolet Instrument Corporation shall notbe liable for errors contained herein nor for incidental or consequential damages in connectionwith the furnishing, performance or use of this material. All product specifications, as well as theinformation contained in this publication, are subject to change without notice.

This publication may contain or reference information and products protected by copyrights orpatents and does not convey any license under the patent rights of Nicolet InstrumentCorporation, nor the rights of others. Nicolet Instrument Corporation does not assume anyliability arising out of any infringements of patents or other rights of third parties.

Nicolet Instrument Corporation makes no warranty of any kind with regard to this material,including but not limited to the implied warranties of merchantability and fitness for a particularpurpose.

Copyright © 1999 by Nicolet Instrument Corporation, Madison WI 53711. Printed in the UnitedStates of America. All world rights reserved. No part of this publication may be stored in aretrieval system, transmitted, or reproduced in any way, including but not limited to photocopy,photograph, magnetic or other record, without the prior written permission of Nicolet InstrumentCorporation.

For technical assistance, please contact:

Customer SupportNicolet Instrument Corporation5225 Verona RoadMadison WI 53711-4495

Telephone: 1-800-NICOLET (1-800-642-6538) or 1-608-276-6373

OMNIC is a registered trademark of Nicolet Instrument Corporation.Nexus, Smart Accessory, Avatar, Continuµm, Smart Purge, OMNI-Transmission, FiberPort,Ever-Glo, Passport, Import, SeaPort, Solid-Substrate, Talon, PLUS, Vectra-Plus, Snap-In,SabIR, Sync and E.S.P. are trademarks of Nicolet Instrument Corporation.Smart Collector, Smart ARK and InspectIR are trademarks of Spectra-Tech, Inc.MIRacle is a trademark of PIKE Technologies.DuraScope and DuraSamplIR are trademarks of SensIR Technologies.Windows is a registered trademark of Microsoft Corporation.Intel and Pentium are registered trademarks of Intel Corporation.PS/2 is a registered trademark of International Business Machines Corporation.

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Contents

Welcome............................................................................................. 1Conventions ................................................................................... 4System requirements...................................................................... 5Where to find the information you need ........................................ 6

Before You Collect Spectra................................................................ 9Checking the purge ...................................................................... 10

Smart Purge settings................................................................ 11Checking the desiccant ................................................................ 12Turning on the system components ............................................. 13Cooling the detector..................................................................... 15Starting OMNIC........................................................................... 16Selecting an experiment............................................................... 17

Your First Experiment...................................................................... 19The OMNIC window ................................................................... 20

Spectral window...................................................................... 20Menu bar ................................................................................. 20Experiment drop-down list box............................................... 21Bench Status indicator............................................................. 21Toolbar .................................................................................... 21

Collecting a sample spectrum ...................................................... 22Installing the standard sample holder...................................... 23Collecting the sample spectrum .............................................. 24

Saving the spectrum..................................................................... 36Converting the spectrum’s units .................................................. 37Labeling a peak with the annotation tool ..................................... 39Verifying the composition of the sample..................................... 42Creating and printing a report ...................................................... 45Adding the spectrum to a user library.......................................... 47Creating a user library.................................................................. 49

Spectrometer Basics ......................................................................... 51Spectrometer components............................................................ 51

What’s inside?......................................................................... 52Viewing the optical layout and beam path in OMNIC ....... 53

What is on the rear panel? ....................................................... 54Turning on the spectrometer power ............................................. 55Using a light source ..................................................................... 58Using beamsplitters and detectors ............................................... 59

Selecting the right beamsplitter and detector .......................... 60Optimizing the performance of your detector ......................... 62

Improving linearity and photometric accuracy ................... 63When to use bandwidth-limiting filters .............................. 64When to use energy screens ................................................ 64What aperture size to use for your detector ........................ 65How to improve the signal-to-noise ratio ........................... 66How to improve the resolution ........................................... 67

How to collect data in the visible spectral range ......................... 68How to collect data in the extended spectral range...................... 69Scan velocities ............................................................................. 71

Slow scan................................................................................. 73A note about vibrations....................................................... 74Running slow-scan experiments ......................................... 74

Using the SST Software ................................................................... 75Starting the SST software ............................................................ 75On-line Help for SST................................................................... 76Collecting data with SST ............................................................. 76Ratioing spectra ........................................................................... 77

Ratioing spectra against a common stored background .......... 77The special case of ratioing only two spectra.......................... 78

Using SST phase array operations ............................................... 79What is a phase array?............................................................. 79What is phase correction?........................................................ 80Phase array operations............................................................. 80

Calculating a phase array .................................................... 81Viewing a phase array......................................................... 83Storing a phase array........................................................... 83Saving a phase array ........................................................... 84

Accessories....................................................................................... 85Smart Accessories........................................................................ 85Other sampling accessories for different applications ................. 88System accessories....................................................................... 92How to cable an accessory ........................................................... 93

Pass-through connectors.......................................................... 93Connectors inside the sample compartment ....................... 94Connectors on the rear panel............................................... 95Using the pass-through connectors for custom

accessories................................................................ 96Detector/Motors connector...................................................... 98

Quick Answers to Your Questions About Using OMNIC............. 101Collecting spectra....................................................................... 101Converting spectra to other units ............................................... 105Using spectral libraries .............................................................. 106Opening, saving and deleting spectra ........................................ 111Printing....................................................................................... 114Displaying spectra...................................................................... 115Correcting spectra ...................................................................... 120Subtracting, adding, multiplying and dividing spectra .............. 121Customizing OMNIC................................................................. 123Other questions .......................................................................... 124

Quick Answers to Your Questions About Using theSpectrometer........................................................... 127

Maintenance and Service................................................................ 131Aligning the spectrometer and accessories ................................ 132

Aligning the spectrometer ..................................................... 132Aligning an accessory ....................................................... 133

Servicing your spectrometer ...................................................... 135

Diagnostics ..................................................................................... 137Checking the performance of spectrometer components........... 137Running the spectrometer performance test............................... 139Performing advanced diagnostics tests ...................................... 141

Using remote diagnostics........................................................... 143Remote diagnostic sessions................................................... 143Modem line specifications .................................................... 144Wall jack specifications ........................................................ 145Running the diagnostics ........................................................ 145About the individual tests...................................................... 146

Rapid scan......................................................................... 146Visible............................................................................... 146AM step scan..................................................................... 147PEM .................................................................................. 148PM step scan ..................................................................... 149SMM ................................................................................. 150TRS ................................................................................... 150

Troubleshooting Software Problems.............................................. 153

Troubleshooting Hardware Problems............................................. 155

Troubleshooting Applications Problems........................................ 161

Index............................................................................................... 165

Nexus 870 User’s Guide 1

Welcome

Congratulations on your purchase of a Nexus 870 spectrometerfrom Nicolet! The spectrometer lets you collect spectra in themid-IR, far-IR and near-IR spectral ranges. The 870 has all of thefeatures of the other Nexus spectrometers, plus step-scan, dualchannel collection and other advanced features. The systemintegrates advanced hardware features with the power and flexibilityof Nicolet’s OMNIC® software*.

This manual explains how to use the system to collect and processFT-IR spectra after it is installed by Nicolet. Included is informationon using your OMNIC software as well as chapters on how tooperate, maintain and service the spectrometer.

*

Some dedicated systems use other Nicolet software packages.

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Warning The Spectrometer Safety Guide that came with your system containsimportant safety information. This guide is available in severallanguages. Contact your local Nicolet office for information about thelanguages that are available. Before using the system, read the entireguide. To prevent personal injury and damage to equipment, follow theprecautions contained in the guide whenever you use the system. ▲

The Nexus 870 has these advanced capabilities:

• Step-scan data collection using either amplitude or phasemodulation.

• Slow-scan linear data collection.

• Dual-channel linear scan PEM (photoelastic modulation) datacollection.

• Optional TRS (time-resolved step-scan) data collection.

• SMM (synchronous multiple modulation) data collection.

This manual explains how to use the system to collect and processFT-IR spectra after it is installed by Nicolet. Included is informationon using your OMNIC software as well as chapters on how tooperate, maintain and service the spectrometer.

If you have not used the spectrometer before, view the“Spectrometer Tour” and “Getting Started With OMNIC” tutorialsavailable through Getting Started in the Help menu of OMNIC.

You can also read the “Before You Collect Spectra” and “Your FirstExperiment” chapters to learn how to start the system and collect andwork with spectra.

See “Where to find the information you need” later in this chapterfor a description of the on-line documentation provided with thesystem and for help finding the answers to your questions.


You can replace key parts of the spectrometer, such as the laser andlight source. Installation instructions are available on-line. See“Where to find the information you need” for details.

Instructions for most accessories are included with the particularaccessory. Additional information on connecting accessories isincluded in this manual.

You can contact Nicolet at the numbers below. Outside the U.S.A.call your local sales or service representative. Telephone numbers forall Nicolet Customer Support offices are provided with your system.

• Telephone (U.S.A.): 1-800-NICOLET (1-800-642-6538)• Fax: 1-608-273-5045• World Wide Web: http://www.nicolet.com• E-mail: [email protected]

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Conventions The following conventions are used in this manual to draw yourattention to the on-line documentation and other importantinformation.

This symbol tells you that you can find more information in the on-line tutorials. To access a tutorial, click the Help menu in OMNIC.

? This symbol tells you that you can find more information in the on-line OMNIC Help or SST Help systems. Choose OMNIC HelpTopics from the Help menu, or choose SST Help Topics from theSST menu.

This symbol tells you that you can find more information in thismanual.

Note Messages like this contain helpful supplementary information abouta procedure or technique. ▲

▲ Caution Follow the instructions given in Cautions to avoid damaging thespectrometer or losing data. ▲

Warning Always heed the Warnings that appear in this manual to avoid beinginjured while using the spectrometer. ▲

Danger Follow the instructions labeled Danger to avoid serious injury or lossof life while using the spectrometer. ▲


System requirements For optimum performance we recommend that your system have, ata minimum, the following items:

• Intel® Pentium® processor with 166 MHz or greater clock speed.• At least 64 megabytes of random access memory (RAM).• The ability to display 16-bit color images.• Hard disk size of at least 1.0 gigabyte.• Quad speed CD-ROM drive.• A 1.44-megabyte floppy disk drive for 3.5-inch floppy disks.• A 15-inch SVGA monitor with 800 by 600 resolution.• A keyboard and serial or bus mouse or PS/2®-style mouse.• 16-bit Sound Blaster compatibility.• Two serial ports.• Two open PCI slots.• One open ISA slot.• Windows® 98 or Windows NT 4.0 or greater.

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Where to find theinformation you need

The on-line and printed documentation included with your system isdesigned to let you find the information you need quickly. Werecommend first using the on-line documentation provided withOMNIC when you have a question. OMNIC includes several on-linetutorials, a wizard and a complete Help system. See “StartingOMNIC” in the next chapter for information on starting OMNIC.

The tutorials teach you how to do these things:

• Use OMNIC features to collect, display and process spectra.

• Set up your spectrometer for a variety of experiments. You canlearn how to change sources, beamsplitters and detectors; installoptical filters and screens; and change the sample compartmentbaseplate.

• Install optional hardware.

• Check and change the desiccant, and purge line filters.

• Change replaceable parts.

• Get part number and ordering information.

Note You must have the Spectrometer Tutorials CD in the computer’sCD-ROM drive to use the “Spectrometer Tour” tutorial or view anyvideotaped parts replacement procedures in the “Spectrometer HelpTopics” tutorial. ▲

You can also find part numbers and hardware setup and replacementprocedures with the computer not connected to the spectrometer.Insert the Spectrometer Tutorials CD into the computer’s CD-ROMdrive and double-click the icon for the P870_ENU.HLP program.


To use a tutorial, choose it from the Help menu or point to GettingStarted, Learning OMNIC or Sampling Techniques in the menu andthen choose the desired tutorial from the list that appears. You canalso start tutorials from within other parts of the on-linedocumentation provided with OMNIC.

SST Help Topics in the SST menu provides complete informationabout setting up hardware and software for SST experiments.

The Library Creation Wizard prompts you, step by step, throughcreating a user library of spectra.

The on-line OMNIC Help system lets you quickly find answers toyour questions about using the software. There are several ways toenter OMNIC Help:

• You can see information about a particular feature in OMNIC(such as a parameter in a dialog box) by clicking the item usingthe right mouse button. A brief description of the item appears,and in most cases one or more buttons that you can click todisplay more detailed information. Here is an example:

Click the Discussion button to display a complete discussion of theitem (or the dialog box or window that contains the feature). Clickthe How To button to display a step-by-step procedure for usingthe item (or the dialog box or window that contains the item).

• You can press the F1 function key to see a discussion topic forthe currently displayed or selected feature, dialog box or window.

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• If a dialog box or window contains a Help button, click it to seeinformation about the dialog box or window (or the commandthat displayed it).

• To see the Contents of the OMNIC Help system, choose OMNICHelp Topics from the Help menu.

Here is an example of the Contents tab showing the contents ofsome of the books in the system:


Before You Collect Spectra

It’s easy to collect spectra with your spectrometer. By leaving thesystem turned on at all times—with the needed components alreadyinstalled—you can keep it ready to use with a minimum ofpreparation. Keeping the system on also improves its stability andgives you more consistent results.

All the things you need to check before collecting spectra are listedbelow; each of these items is discussed in a section of this chapter.By the time you have run through these items once or twice in thecourse of your work, you will know how to check the system andstart collecting spectra quickly.

• Check the purge or desiccant.• Make sure the system components are on.• Cool the detector (if you are using an MCT, InSb or other

detector that requires cooling with liquid nitrogen).• Start OMNIC and select an experiment.

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Checking the purge

Skip this section if you purchasedthe “Sealed and Desiccated” option.

If your spectrometer is purged but you don’t have the Smart Purgeoption, make sure the pressure regulator is set between 20 and 40pounds per square inch (psi) and the flowmeter reads approximately30 standard cubic feet per hour (scfh). The settings for Smart Purgeare given in the next section; read this section first.

If you need to adjust the flow rate, or if your application requires adifferent flow rate, follow the instructions in “Setting the purge gascontrols” in the “Setting up experiments” book in Spectrometer HelpTopics.

Warning Never use a flammable gas to purge the spectrometer. The purge gasmust be free of moisture, oil, carbon dioxide and other reactive orinfrared-absorbing materials. Use dried air or nitrogen to purge thespectrometer. Other gases, even inert gases such as argon, can damagethe spectrometer and should never be used for this purpose. ▲

50

40

302010

SCFH AIR80

100

120

140

1600

20

40

60

We recommend that you leave the purge on at all times. This keepsthe spectrometer free of undesirable gases, protects the optics andimproves the system’s thermal stability.


In Spectrometer Help Topics view “Maintaining your spectrometer”for information on how to install the purge equipment, set thecontrols for the first time, and inspect and clean the purge filter. Inthe Spectrometer Tour (available through Getting Started) view“Sample compartment” for information on using Smart Purge.

Smart Purge settings The Smart Purge option increases the purge gas flow rate when youinstall or remove samples. If you have this option, set the pressureregulator to 80 psi. The auxiliary tank may be required depending onthe flow rate supplied by your purge gas source. See the followingtable for details.

Flow Rate* Tank Required? Comments

less than50 scfh

yes Some purge gas and pure airgenerators provide a flow rate ofless than 50 scfh.

50-99 scfh optional Using the tank will improveperformance.

100 scfh orgreater

no A flow rate of 100 scfh gives thebest results.

* Flow rates greater than 50 scfh cannot be measured with the flowmeter installed byNicolet. See your air dryer manual or contact the department that maintains your purgeequipment if you don’t know the flow rate of the purge gas source.

? You can use OMNIC to set the duration of increased purge flow. InOMNIC Help Topics find “purge” in the Index and go to “SettingSmart Purge.”

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Checkingthe desiccant

If your spectrometer is sealed and desiccated, a bag of desiccant islocated under the beamsplitter compartment cover. The desiccantprotects the beamsplitter and other optical components by reducingthe amount of water vapor inside spectrometer. See “Checking andchanging desiccant” in the “Maintaining your spectrometer” book inSpectrometer Help Topics if you need to change the desiccant.

If your spectrometer is in use, check the humidity level inside itmonthly (more often in very humid climates) by clicking the CheckDesiccant button on the Diagnostic tab of the Experiment Setupdialog box. If the level exceeds the factory-specified limit, a messageinforms you. Be sure to change the desiccant so that the optics willbe protected.

If your spectrometer is in storage, check the round, blue indicator onthe desiccant holder under the beamsplitter compartment covermonthly. Change the desiccant if the indicator has turned pink. Keepall covers closed tightly while the spectrometer is in storage.

Note The Check Desiccant button measures humidity more accuratelythan the indicator. For this reason you should rely on the button tomonitor the performance of the desiccant when the spectrometer is inuse. Rely on the indicator only when the spectrometer is in storage. ▲

? See “Ordering parts” in Spectrometer Help Topics to find the partnumber for ordering desiccant bags.


Turning on thesystem components

We recommend that you keep your spectrometer on at all times,unless the building is subject to power outages or you need toperform a service or maintenance procedure. Leaving the system onkeeps it stable and gives you the most consistent results. If you mustturn the spectrometer off, allow it to stabilize for at least 15 minutes(one hour for best results) before collecting spectra.

Follow these steps to turn on the system components:

1. If the external power supply is not already connected,connect it.

In the Spectrometer Tour (available through Getting Started)view “Connecting to AC power” in the “Powering up” unit forinformation on connecting the power supply.

2. Turn on any accessories you plan to use.

This includes accessories such as a gas chromatograph, a GCinterface or an infrared microscope.

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Warning Always follow the safety precautions described in this manual and inthe Spectrometer Safety Guide that came with your system. ▲

3. Turn on the spectrometer by pressing the power switch (I/O)on the external power supply to I.

Power switch

When you turn on the spectrometer, the four status indicators—Power, Scan, Laser and Source—flash in various sequences asthe system runs through its diagnostic routines. When theroutines are finished, the Power, Laser and Source indicators staylighted. The Scan indicator flashes with each scan of theinterferometer.

After you turn on the spectrometer, let it stabilize for at least15 minutes (one hour for best results) before collecting spectra.

See “Turning on the spectrometer power” in the “SpectrometerBasics” chapter if you need more information.

4. Turn on the printer and then the computer.

Turn on the printer and computer as explained in thedocumentation that came with those components.


Reverse the order given in the preceding procedure when you turnoff system components:

1. Turn off the computer.2. Turn off the printer.3. Turn off the spectrometer.4. Turn off the accessories.

Cooling the detector Some detectors, such as an MCT or InSb detector, require coolingwith liquid nitrogen. In Spectrometer Help Topics view “Cooling adetector” in “Setting up experiments” for instructions.

Warning Liquid nitrogen is extremely cold and therefore potentiallyhazardous. Avoid contact with skin. Wear protective clothing andfollow standard laboratory safety practices to prevent injury. ▲

After you fill the detector dewar with liquid nitrogen (the dewarholds about 750 mL), allow the detector to cool at least 20 minutesbefore collecting spectra.

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Starting OMNIC Follow these steps to start OMNIC:

1. Start the Windows software.

2. Double-click the OMNIC E.S.P. shortcut.

The shortcut is onthe Windows desktop.

Depending on how the program has been configured, dialogboxes may appear asking for a user name and password. Typeyour user name if requested, and then choose OK. Enter apassword if required.

The OMNIC window appears. This window is described in thenext chapter.


Selectingan experiment

By selecting an experiment from the Experiment drop-down list boxbelow the OMNIC menu bar, you can quickly set the softwareparameters for the type of data collection you want to perform.

A number of experiments are provided with OMNIC, and you cancreate and save your own. If you install a Smart Accessory, thecorrect experiment is selected automatically (or a list of appropriateexperiments is made available for your selection).

In the tutorial in the next chapter the provided Default - Transmission(or Transmission E.S.P.) experiment is used. You will probably findthat this experiment is suitable for most of your applications.

If you want to check or change the parameters after selecting anexperiment, use Experiment Setup in the Collect menu.

You are now ready to collect spectra.

To learn more about experiments, see “Opening an experiment” inthe “Preparing the software” unit of Collecting a Spectrum (availablethrough Learning OMNIC). If you need to install or change a source,beamsplitter or detector for your experiment, follow the instructionsin “Setting up experiments” in Spectrometer Help Topics.

Note The most commonly used hardware configuration for mid-IRexperiments includes a KBr beamsplitter, an Ever-Glo (mid-IR tofar-IR) source and a DTGS detector. You may need to change thesettings of the example experiment if your hardware configuration isdifferent. ▲

If you have not used the system before, you can learn how toperform an experiment by viewing Collecting a Spectrum (availablethrough Learning OMNIC) or by using the tutorial in the nextchapter of this manual.

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Your First Experiment

This chapter will get you started collecting spectra with yourspectrometer and working with the data using OMNIC. You willlearn how to do the following things:

• Open a configuration.• Select an experiment and check the parameters.• Install a sample and collect a sample spectrum.• Save the spectrum.• Convert the spectrum to other units.• Label a peak in the spectrum.• Verify the composition of the sample by comparing the spectrum

with spectra in a QC library.• Create and print a report containing the spectrum.• Add the spectrum to a user library.• Create a user library.

You can learn all these things and more by running the on-linetutorials provided with OMNIC. Start with the Spectrometer Tourand Getting Started With OMNIC (available through GettingStarted).

Follow the instructions in the preceding chapter to prepare thesystem and start OMNIC before using this chapter.

Note If you have a dedicated system (such as an ECO/RS) that normallyuses a software package other than OMNIC, skip this chapter. Seethe special documentation that came with your system forinstructions on using that software. If you need information on usingthe spectrometer, see the chapters that follow this one. ▲

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The OMNIC window The large window that appears on the screen when you start OMNICis called the OMNIC window.

Spectral window

Experiment drop-downlist box Menu bar Toolbar

Bench Statusindicator

Spectral window Within the OMNIC window is a spectral window, which you can useto display and manipulate spectra. When a spectrum is displayed in aspectral window, you can use OMNIC commands to performoperations on it. For example, you can change the spectrum’s formator search it against a spectral library to identify it.

Menu bar Below the title bar is the menu bar, which contains all of the OMNICmenu names. The menus are arranged in an order that you’ll findconvenient as you use the software. All of the menu commands areexplained in detail in the on-line tutorials or the OMNIC Help system.


Experimentdrop-down list box

Below the menu bar is the Experiment drop-down list box. TheExperiment drop-down list contains all of the experiment files youhave opened, plus the default experiment file and an experiment filefor any Smart Accessory you have installed. By selecting anexperiment with this feature, you can quickly set the softwareparameters for the type of experiment you want to perform. You cansee the parameter settings for the selected experiment by usingExperiment Setup in the Collect menu.

Bench Status indicator To the right of the Experiment drop-down list box is the BenchStatus indicator.

If the indicator is a green check mark, the spectrometer has passedall of its diagnostic tests.

If the indicator is a yellow circle, a cooled detector in thespectrometer has become warm. A message appears explaining theproblem and allowing you to access information on correcting it.

If the indicator is a red X, the spectrometer has failed a diagnostictest and requires corrective action. A message appears explaining theproblem and allowing you to access information on correcting it.

Note If you want to view the on-line videos to help troubleshoot aproblem, put the Spectrometers Tutorials CD into the computer’sCD-ROM drive. ▲

Toolbar Below the Experiment drop-down list box is the toolbar. Each buttonin the toolbar represents a menu command, a macro or an externalprogram. To see the name of the command or feature for a button,point to the button and wait a moment. To initiate the command orfeature, click the button with the left mouse button.

? In OMNIC Help Topics find “toolbar” in the Index and go to“Displaying and using a toolbar” for information on using andcustomizing the toolbar buttons.

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Collecting asample spectrum

A sample spectrum is usually ratioed against a background spectrum.The background spectrum measures the response of the spectrometerwithout a sample in place. Dividing the sample spectrum by thebackground—called “ratioing”—removes the effects caused by theinstrument and atmospheric conditions so that the peaks in the finalspectrum are due solely to the sample.

Here is a typical background spectrum:

For most applications you don’t need to collect a new backgroundspectrum for each sample spectrum if you haven’t changed thesoftware parameters. To obtain good results, however, collect a newbackground regularly, perhaps once every four hours. (You canobtain the best results by collecting a new background for eachsample, but this is seldom necessary.)


Installing thestandard sample holder

If the standard sample holder is not already installed, install it now.The following illustration shows the sample holder in place.

Heightadjustment

screw

Sampleholder

Accessorysupport

If you are using separate Snap-In™ sample compartment baseplatesfor different accessories and sample holders, you can quickly switchbaseplates to install the sample holder. For information on usingSnap-In baseplates, view “Removing the Snap-In baseplate” in“Setting up experiments” in Spectrometer Help Topics.

If your sample holder is mounted on a Smart baseplate, theTransmission E.S.P. experiment is automatically selected when youinstall the baseplate in the sample compartment.

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If your sample holder is not installed on a baseplate, use a flat-bladescrewdriver and the slotted screws to attach the holder to a baseplateas shown below. Then install the baseplate in the samplecompartment.

If there is a sample in theholder, remove the sample.

To install a sample or filter, slide the sample or filter into one pair ofslots. If the accessory support is currently installed in the slot youwant to use, remove the support before installing the sample or filter(see the first illustration in this section). Replace the support whenyou are finished using the slot. Do not discard the support; it isneeded for installing slide-mounted accessories.

Collecting thesample spectrum

In the data collection procedure that follows, you will collect abackground spectrum and then a spectrum of the providedpolystyrene sample. Before collecting the spectra, you will open aconfiguration that sets a number of software options for thisprocedure.

You can also learn how to collect spectra by viewing Collecting aSpectrum (available through Learning OMNIC).


Follow these steps:

1. Choose Open Configuration from the File menu.

The Open Configuration dialog box appears listing the availableconfiguration files. Opening one of these files lets you quicklyset a number of software options.

2. Select the DEFAULT.CON file and then choose OK.

This file was provided with your OMNIC software for setting theoptions for this procedure.

3. Select the Default - Transmission experiment (or theTransmission E.S.P. experiment).

Both of these experiments set the parameters correctly forcollecting a polystyrene sample spectrum. If either of them isalready selected, you do not need to select an experiment. Thecurrently selected experiment is shown in the Experiment boxnear the top of the OMNIC window.

To select the Default - Transmission (or Transmission E.S.P.)experiment, first click the arrow button at the right end of theExperiment drop-down list box. The Default - Transmission (orTransmission E.S.P.) experiment appears in the list.

Select the Default -Transmission (or Transmission

E.S.P.) experiment by clicking it.

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A number of other experiments are provided with OMNIC forperforming a wide variety of data collections. You can selectthese experiments by using the Open button in the ExperimentSetup dialog box. After you have selected one of them the firsttime, the experiment will appear in the Experiment drop-downlist for future selection. You can also set up and save your ownexperiments.

4. Check the settings of the parameters by choosing ExperimentSetup from the Collect menu.

This step is normally not necessary, but it’s a good way tobecome familiar with the parameters. The Experiment Setupdialog box appears.

If data collection parameters shown below are not alreadydisplayed, click the Collect tab to display them.


?

The data collection parameters, along with the other experimentparameters, determine how OMNIC collects background andsample spectra. In OMNIC Help Topics find “experiment” in theIndex and go to “Using Experiment Setup” for more information.

Notice that the Collect Background Before Every Sample optionis selected. This option prompts you to collect a backgroundspectrum before you collect a sample spectrum.

The File Handling box contains options for saving dataautomatically. When Save Automatically is on, OMNIC savescollected spectra immediately after collection, naming the filesusing the base name specified in the Base Name box plus asequence number with up to four digits, followed by an extensionsuch as .SPA for spectra. The files are saved using the pathshown below the base name.

If Save Interferograms is on, the interferograms for your spectraare saved when you save the spectra. Interferograms are the rawspectral data. Saving them allows you to reprocess a spectrumlater in case you want to restore it after performing corrections orother operations on it.

?

Leave the options in the File Handling box as they are for thisprocedure. In OMNIC Help Topics find “file” in the Index andgo to “File handling” if you want more information on the FileHandling options.

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Click the Bench tab to display the spectrometer parameters.

Verify that the Beamsplitter, Detector and Source settings matchthe components you have installed in your system.


Click the Quality tab to display the spectral quality checks.

The selected checks on this tab are performed automaticallyduring data collection. (In the Default - Transmission experimentthe checks are turned off.) If a problem is found by a check, thesoftware informs you and provides information to help youcorrect the problem. This is explained in more detail later in thisprocedure.

5. Choose OK to close the Experiment Setup dialog box.

You are now ready to collect a spectrum of the providedpolystyrene sample.

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6. Click the Collect Sample button in the toolbar.

You can also choose CollectSample from the Collect menu.

The Collect Sample window appears and then a dialog boxshowing the default title for the sample spectrum:

7. Type a title in the text box or choose OK to accept the default.

Since the experiment you are using specifies that a backgroundshould be collected before every sample, a message appears nowasking you to prepare to collect a background spectrum.

This means that you need to remove any sample from the sampleholder so that the beam path is clear. When you then collect abackground spectrum, the result is a measurement of theresponse of the spectrometer alone; that is, without absorptionsdue to a sample.


8. Look through the sliding door to make sure there is nosample in the sample holder and then choose OK to startdata collection.

If there is a sample in the sample holder, remove it beforechoosing OK:

If your spectrometer is purged but does not have the Smart Purgeoption...

Open the sliding door, remove the sample, close the slidingdoor and then wait 1 minute before choosing OK.

If your spectrometer has the Smart Purge option...

Open the sliding door, remove the sample and then slide thedoor until it is open about 1 cm. When you hear the purgeflow rate return to normal, close the door all the way andchoose OK.

If your spectrometer is sealed and desiccated...

Open the sliding door, remove the sample, close the slidingdoor and then choose OK.

A background spectrum appears in the Collect Sample window.The spectrum is updated as more data are collected. When all thebackground data have been collected, a message appears askingyou to prepare to collect the sample spectrum:

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9. Install the polystyrene sample through the sliding door, waitif necessary (see the instructions below) and then choose OK.

If your spectrometer is purged but does not have the Smart Purgeoption...

Open the sliding door, install the sample, close the slidingdoor and then wait 1 minute before choosing OK.

If your spectrometer has the Smart Purge option...

Open the sliding door, install the sample and then slide thedoor until it is open about 1 cm. When you hear the purgeflow rate return to normal, close the door all the way andchoose OK.

If your spectrometer is sealed and desiccated...

Open the sliding door, install the sample, close the slidingdoor and then choose OK.


For more information on installing samples, view “InstallingSamples” in the Spectrometer Tour (available through GettingStarted).

As data are collected, the sample spectrum in the Collect Samplewindow is updated. Here is the Collect Sample window duringsample data collection:

The progress of the collection is indicated visually by the gaugeabove the tool palette. The number of scans collected so far andthe total number of scans for the collection are displayed to theright of the gauge.

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The Collect Status indicator above the view finder shows thestatus of the collection during and after collection. When theindicator is a green check mark, it shows that the spectrum haspassed all of the selected spectral quality checks made so far.After the collection is finished and the indicator is a green checkmark, you can add the spectrum to a spectral window (if it is notadded automatically).

If you ever have a problem with data collection while one ormore quality checks are turned on, the Collect Status indicatormay change. If the indicator is a yellow circle, the spectrum hasfailed a spectral quality check (a measured value was not withinthe allowed range), but it is not serious enough to stop thecollection. If the indicator is a red X, there is a problem with thequality of the spectrum. After correcting the problem, collect thespectrum again.

To view information about the collection, including any problemsthat have occurred, click the indicator during or after the collection,or click the View Collect Status button as explained below.

When all the sample data have been collected, the followingmessage appears asking whether to add the spectrum to a spectralwindow:

Choosing View Collect Statusdisplays the Results window,

which shows a summary ofproblems encountered and otherinformation about the collection.

Clicking the View Collect Status button displays the Resultswindow, showing a summary of any problems encounteredduring data collection and other information about the collection.


10. Choose Yes to add the sample spectrum to the spectralwindow.

Choosing No ends the procedure without saving the spectrum.Choosing Cancel returns you to the Collect Sample window,allowing you to collect more scans with the More button.

Here is the sample spectrum displayed in the spectral window:

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Saving the spectrum You can save your spectrum manually on the hard disk by usingeither of two commands in the File menu: Save or Save As. UseSave when you want to save a spectrum on the disk using the currentfilename and path. In this example you will use Save As to save aspectrum in a file on the disk using a new filename.

Follow these steps to save the polystyrene spectrum you justcollected:

1. Select the polystyrene spectrum by clicking it.

2. Choose Save As from the File menu.

The Save As dialog box appears.

3. Type the name POLY.SPA following the directory path inthe File Name box.

The text can be either upper or lower case. The default directorypath for saving files is determined by the settings on the File tabof the Options dialog box, available through Options in the Editmenu.

4. Choose OK.

If you typed a filename that already exists in the directory, amessage appears asking whether to replace the existing file.Choose No and then use a different filename to save thespectrum.

In the next section, you will convert the spectrum to% transmittance and back to absorbance.


Converting thespectrum�s units

The sample spectrum you collected is in absorbance units. Since manyof OMNIC’s data manipulation commands work best on spectra inabsorbance units, it is often useful to convert a spectrum to absorbanceby using the Absorbance command. In this example you will convertthe spectrum to % transmittance and then back to absorbance.

1. Select the spectrum by clicking it.

2. Click the % Transmittance button in the toolbar.

You can alsochoose % Transmittancefrom the Process menu.

The spectrum is converted to % transmittance units:

Spectrum in % transmittance units

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?

The Process menu allows you to convert spectra to several otherunits as well. These units are discussed in detail in the OMNICon-line Help system. In OMNIC Help Topics find “convertingspectrum” in the Index and go to the topic that deals with theunits you are interested in.

3. Click the Absorbance button in the toolbar to return thespectrum to absorbance units.

You can also chooseAbsorbance from the Process menu.

In the next section, you will label a peak in the absorbancespectrum using the annotation tool.


Labeling a peak withthe annotation tool

The palette contains six tools that let you select a spectrum orspectral region, change how spectra are displayed in a spectralwindow, find the height or area of a peak, or label a peak. The namesand appearance of the palette tools indicate their functions.

Peak height

Selection

Region

Spectral cursor Peak area

Annotation

Follow these steps to label a peak in the polystyrene spectrum:

1. Select the annotation tool by clicking it.

The annotation tool lets you label peaks with their frequencylocations (X values) or other information.

Only one tool can be used at a time. To use a tool, first select it byclicking it. A tool remains selected until you select another tool.

When you use a tool, the readout above the palette may displayinformation for the tool operation; for example, the X and Yvalues of the pointer location or the limits of the selected spectralregion. Here is an example of X and Y values displayed in thereadout when the selection tool is selected and the pointer iswithin a pane of a spectral window:

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When the annotation tool is selected and you move the pointerinto a pane of a spectral window, the pointer looks like this:

You can label a peak by clicking above it with the annotationtool. This displays the label text above the peak with a lineconnecting the label to the peak. The text is selected so that youcan immediately edit it. When you press Enter, the label appearsin its final form.

You can more accurately locate the top of a peak by holdingdown the Shift key when you click near the peak.

2. Label the peak near 2,924 wavenumbers by holding down theShift key and clicking a little above the peak.

The label appears:


3. Press Enter to accept the label text.

You could also perform other operations on the label using theannotation tool. To modify a newly created label, edit theselected text before pressing Enter. To modify an existing label,click it and then type a new label and press Enter. To delete anexisting label, click it and then press the Delete key.

? In OMNIC Help Topics find “tool, annotation” in the Index andgo to “Annotation tool” for more information on the annotationtool.

In the next section, you will compare the spectrum with thespectra in a QC library to verify the composition of the sample.

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Verifying thecomposition

of the sample

You can verify the composition of your polystyrene sample byautomatically comparing the collected spectrum with the spectra in aQC (Quality Control) library. The software compares the samplespectrum with reference spectra in the appropriate category in thelibrary and then tells you whether the sample matches a libraryspectrum.

Note If you were unsure of the composition of the sample, you couldperform a “spectral search” using a search library. In that case, thesoftware would search the library and then display a list of thelibrary spectra that best matched the unknown spectrum. ▲

Follow these steps to perform a QC comparison:

1. Select the spectrum by clicking it.

2. Choose Library Setup from the Analyze menu.

The Library Setup dialog box appears with the Search Librariestab displayed.


The Library Directories box lists the directories that are currentlybeing used for spectral searches and QC comparisons. All thelibraries in the listed directories are available for your QCcomparison.

3. Add the LIBS directory (within the OMNIC directory) to thelist of directories if it is not already in the list.

This is the directory that contains the provided PolystyreneQuality Control Sample library. To add the directory to the list,choose Add Directory. In the dialog box that appears, locate andselect the LIBS directory, and then choose OK.

4. Click the QC Libraries tab to display the available QClibraries.

The available QC libraries appear in the Available QC LibrariesAnd Groups box.

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The libraries listed in the QC Libraries And Groups box are thelibraries with which your spectrum will be compared.

5. Add the Polystyrene Quality Control Sample library to thecomparison list.

To do this, click the Polystyrene Quality Control Sample libraryin the Available QC Libraries And Groups box, and then clickthe Add button.

6. Choose QC Compare in the Library Setup dialog box to startthe comparison.

You can also close the Library Setup dialog box and begin a QCcomparison at any time by choosing QC Compare from theAnalyze menu.

When you begin a comparison, the QC Compare windowappears. At the bottom of the window a gauge shows theprogress of the comparison.

When the comparison is finished, the sample spectrum and thelibrary spectrum that best matches it are displayed in panes in theupper portion of the window. Comments about the comparisonappear in the lower portion of the window. In this example thecomparison found that the sample spectrum matches thepolystyrene spectrum in the library.

7. Close the QC Compare window by choosing Close.

? In OMNIC Help Topics find “QC comparison” in the Index andgo to “Performing a QC comparison” if you want moreinformation about comparing sample spectra with QC libraries.


Creating andprinting a report

OMNIC makes it easy to create and print a report containing theresults of your work. Follow the steps below.

You can also view Creating Reports (available through LearningOMNIC) to learn how to create and print reports and add them toreport notebooks.

1. Choose Template from the Report menu.

A dialog box appears allowing you to locate and select a reporttemplate for the report.

2. Go to the REPORT directory (within the OMNIC directory)and select the report template file named QCCOMP.RPT.

This file contains a report template specially set up for thisprocedure. The template has items for the spectral window,spectrum time, title and comments, and search results.

When you select the report template file, a preview image of thetemplate appears at the right. This feature allows you to see whatdifferent templates look like so that you can pick one with theitems you need. You can view the image as a graphical layout byselecting the Layout option. This shows you how the printed reportwill look on paper. You can also view the image with templateitems labeled by selecting the Description option. This lets youidentify items that are too small to be seen clearly.

3. Choose Select to make the example template the currenttemplate for printing reports.

When you print your report, OMNIC will automatically fill in theitems with the appropriate information and images. For example, ifan item in the template is linked to the active spectral window, thecontents of that window are included when you print the report.

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?

You can create your own report templates by using the Createbutton, or you can modify one of the existing templateswhenever you want to design a new template. Save the templatewith a new name after you make your changes. In OMNIC HelpTopics find “report template, selecting” in the Index and go to“Selecting, editing or creating a report template” for moreinformation on using reports.

4. Choose Preview/Print Report from the Report menu.

A preview of the report appears showing the report items filled inwith information about your spectrum. Your report should looksimilar to this:

You can click the Zoom button tosee an enlarged image of the report.

The preview lets you check the content of the report beforeprinting it.


5. If you have a printer connected to the computer, choose Printto print the report.

The Print dialog box appears allowing you to set someparameters that affect printing.

6. Choose OK.

The report is printed on your system printer.

Adding thespectrum to

a user library

You can save your spectrum in a user library even if you have savedit in a spectral data file. This allows you to find the spectrum later bysearching for text contained in the information saved with thespectrum. If you add your own reference spectra collected from puresample materials to a user library, you can also use the library toidentify unknown spectra.

Follow these steps to add the polystyrene spectrum to a user library:

1. Select the polystyrene spectrum.

2. Choose Add To Library from the Analyze menu.

The Select Library dialog box appears listing all the user librariesavailable in the currently specified library directories of the harddisk.

3. Select the User Example Library.

This library has been created for you to use in this example.

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4. Choose OK.

The Add To Library dialog box appears showing the name of thelibrary you selected and the index number that has been assignedto the spectrum. The dialog box also contains fields into whichyou can enter information about the spectrum. The first fieldalready contains the compound name. You can accept or changethe text in the fields.

5. When you have finished entering information about thespectrum, choose OK.

You can also add a spectrum to a library by dragging thespectrum or the spectrum’s file to the library’s book on theLibrary Names tab of Library Manager.

? In OMNIC Help Topics find “user library, adding spectrum to”in the Index and go to “Adding user library spectra to anotheruser library” for more information on options for adding spectrato libraries.


Creating auser library

Creating your own library lets you customize the information in thelibrary depending on your search needs. You can create a searchlibrary for identifying unknown spectra, a QC library for verifyingthe composition of a sample, or a scrapbook library for storingspectra to be retrieved later.

When you create a user library, you determine the kinds of informationthat will be saved with it. You also set a number of parameters,including the resolution and spectral range of the library and whichchecks and corrections are performed. The Library Creation Wizardleads you through the steps that are appropriate for the type of libraryyou are creating.

Once a library is created, you can add spectra to it with the Add ToLibrary button (or with Add To Library in the Analyze menu) anduse it just as you would a commercial library to identify unknownspectra or verify the composition of a sample. If you create ascrapbook library, you can find spectra in it by searching for text.

In this example you will create a new search library. Follow thesesteps:

1. Choose Library Manager from the Analyze menu.

Library Manager appears with the Library Names tab in front.

2. Choose Create Library.

The Library Creation Wizard appears.

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3. In the Library Creation Wizard, select Search Library, andthen enter a name and filename.

The name you enter for the library will appear in the LibraryNames list when you add a spectrum to a library. You can enter anew filename or accept the default name the Wizard assigns.Click Next to continue.

4. In the next dialog box, enter any comments you wish torecord and your name.

The comments you enter will appear in the Comments box on theLibrary Info tab of Library Manager when you select the libraryon the Library Names tab. The name you enter will appear in theCreated By readout on the Library Info tab when you select thelibrary on the Library Names tab.

5. Add more information about your library.

You can continue entering information about the new library byclicking Next. The Wizard lets you enter information aboutspectral range, resolution and blanked areas for searching. Forthis example, click Next in each window.

6. When you have completed entering information, click Finish.

When you click the Finish button, your library is created. Youcan see the library listed by clicking the Search Libraries book onthe Library Names tab of Library Manager.

? In OMNIC Help Topics find “library, creating” in the Index andgo to “Creating a user library” for more information on creatinglibraries.


Spectrometer Basics

This chapter describes the major components of your Nexus 870spectrometer, including the light source, beamsplitter and detector. Itthen explains what you will need to know before collecting data invarious spectral ranges.

In the Spectrometer Tour (available through Getting Started) view“From the front,” “The back panel” and “Inside the spectrometer”for complete descriptions of your spectrometer’s internal andexternal components.

Spectrometercomponents

The following illustration identifies some major components visibleon the outside of the spectrometer.

Status indicators

SST connectors

Detector fill ports

Detectorcompartment

Sliding door

Samplecompartment

External beam port

Emission port forexternal source

Beamsplittercompartment

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? Choose SST Help Topics from the SST menu to find completeinformation about using the SST connectors.

What�s inside? The illustration below shows a top view of the optical layout of thespectrometer with covers removed to reveal components.

Electronics

Front detector

Detectormirror

Backdetector

Externalbeam port

Interferometer BeamsplitterLaser

Beamsplitterstorage

Fixed mirroror optionalemission optics

Externalemission port

Passport optics(optional)

Externalbeam port

Aperture

Infrared source

Fixed mirror or optionalSeaPort optics

Near-IR source

Samplecompartment

Sample holder Energy screenor filter (optional)

In the Spectrometer Tour (available through Getting Started) view“Inside the spectrometer” for complete descriptions of yourspectrometer components.


Viewing the optical layoutand beam path in OMNIC

The beam path isindicated by a thick red line.

You can view an image of the optical layout showing the currentbeam path through the system by choosing Show Optical Layoutfrom the Collect menu. Here is an example:

You can select a different view of the layout from the Viewpointdrop-down list box. If you click the left or right arrow buttons, theview changes in steps.

To see what type of detector or source is installed in a location, movethe mouse cursor over the image of the component. To select adetector or source, click it. The beam path changes to reflect yourselection.

? In OMNIC Help Topics find “optical layout” in the Index and go to“Displaying the optical layout” for a complete description of thisfeature.

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What is onthe rear panel?

The illustration below shows the locations and uses of the connectorsand the reset button on the spectrometer rear panel:

Connectors forcontrolling external

accessories

Connector for cablefrom computer

Resetsspectrometer

Connector for RemoteSignals Accessory

Connector for externalDC power supply

Optional connectors forpassing signals between

rear panel and samplecompartment

Warning Improper or unsafe cabling can cause damage to system hardwareand may create a safety hazard. Nicolet is not responsible for damageor injury resulting from improper or unsafe cabling. ▲

Note Use the Reset button when you are instructed to reset thespectrometer by the troubleshooting procedures found in this manualand elsewhere in the system documentation. ▲

In the Spectrometer Tour (available through Getting Started) view“The back panel” for complete descriptions of the rear panelcomponents.

For more information about the Auxiliary pass-through connectors,see the “How to cable an accessory” section of the “Accessories”chapter.


Turning on thespectrometer power

Follow these steps to turn on the spectrometer power:

1. If the external power supply is not already connected,connect it.

In the Spectrometer Tour (available through Getting Started)view “Connecting to AC power” in the “Powering up” unit forinformation on connecting the power supply.

2. Turn on any accessories you plan to use.

This includes accessories such as a gas chromatograph, a GCinterface or an infrared microscope.

Warning Always follow the safety precautions in this manual and in theSpectrometer Safety Guide that came with your system wheneveryou use the spectrometer. ▲

3. Turn on the spectrometer by pressing the power switch (I/O)on the external power supply to I.

To turn the spectrometeroff, press the switch to O.

Power switch

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When you turn on the spectrometer, the four status indicators—Power, Scan, Laser and Source—flash in various sequences asthe system runs through its diagnostic routines. When theroutines are finished, the Power, Laser and Source indicators staylighted. The Scan indicator flashes with each scan of theinterferometer.

Note After you turn on the spectrometer, let it stabilize for 15 minutes(one hour for best results) before collecting data. Leave thespectrometer on at all times, unless the building is subject to poweroutages or you need to perform a service or maintenance procedure.Leaving the spectrometer on increases stability and consistency ofperformance. ▲

4. Turn on the printer and then the computer.

Turn on the printer and computer as explained in thedocumentation that came with those components.

Reverse the order given in the preceding procedure when you turnoff system components:

1. Turn off the computer.2. Turn off the printer.3. Turn off the spectrometer.4. Turn off the accessories.

In the Spectrometer Tour (available through Getting Started) view“Powering Up” for complete instructions on turning on your system.

Note The system enters a “long-stroke” mode 10 minutes after datacollection activity has ceased. This mode continues for 1 hour. After1 hour, the interferometer stops scanning and the Scan light stays on.Any data collection activity will cause the interferometer to beginscanning. Exiting OMNIC also activates the long-stroke mode. ▲


Note If the Power, Laser or Source indicators flash or will not light at all,or if the Scan indicator will not light, the Bench Status indicator willshow a red X and troubleshooting tips will appear on the screen. Ifyou cannot resolve the problem by following these tips, by pressingthe Reset button on the rear panel or by turning the spectrometerpower off and then on, contact Nicolet at one of the numbers below.Outside the U.S.A. call your local sales or service representative.Telephone numbers for all Nicolet Customer Support offices areprovided with your system.

• Telephone (U.S.A.): 1-800-NICOLET (1-800-642-6538)• Fax: 1-608-273-5045• World Wide Web: http://www.nicolet.com• E-mail: [email protected] ▲

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Using a light source The Nexus 870 has an IR source and a near-IR source. You canswitch between different internal sources simply by changing theSource setting on the Bench tab of the Experiment Setup dialog box.This option lets you collect spectra in the mid-IR to far-IR range orin the visible to near-IR range. The spectral range is determined bythe source, beamsplitter and detector you are using.

In Spectrometer Help Topics view “Installing a new source” in“Setting up experiments” if you need to install or change a source.

Warning Even after the spectrometer is turned off, the external housings ofworking IR sources remain hot for up to 15 minutes. To avoid beingburned by a currently installed source, allow enough time for it tocool before handling it. ▲

Nexus 870 spectrometers with the emission accessory can use anexternal source if one is available. The beam from the externalsource passes through the emission port on the right side of thespectrometer.

? In OMNIC Help Topics find “source” in the Index and go to“Specifying the source type” for instructions on using differentsources in your spectrometer.


Using beamsplittersand detectors

A number of beamsplitters and detectors are available for use in theNexus 870. Not all beamsplitters and detectors can be used together.Some detectors can accommodate only a portion of the energy fromthe source and require changing the aperture size or installing anenergy filter. This section explains how to select and optimize theperformance of beamsplitters and detectors.

In Spectrometer Help Topics view the appropriate lesson in “Settingup experiments” if you need to install or change a beamsplitter ordetector.

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Selecting the rightbeamsplitter and detector

There are two considerations when selecting a beamsplitter-detectorcombination: compatibility and spectral range.

The following table shows which beamsplitter-detector combinationsperform best and which are compatible. Combinations areconsidered compatible if they provide a detector signal that is largeenough to allow the beamsplitter to be aligned. This does notnecessarily mean a particular combination will provide themaximum capable sensitivity range of each component.

DETECTOR

BEAMSPLITTER

DTGS(KBr window)**

DTGS(Csl window)

DTGS(PE window)

MCT-A

Quartz CaF2 XT-KBr KBr Csl Solid Substrate

Near-IR Mid-IR* Far-IR

MCT-B

InSb

PbSe

Si

PbS

InGaAs

OK

X

X

X X OK Best

OK OK Best X

X Best Best OK X

OK

OK

OK

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

XXX

Best

Best

Best

Best

OK OK

OKOK

Best

Best

OK

OK OK

X

X

OK

OK

OK

Best

Best

OK

Best

Best = Optimum beamsplitter-detector combination.OK = Compatible beamsplitter-detector combination.X = Incompatible beamsplitter-detector combination.

* A ZnSe beamsplitter may also be used as a mid-IR beamsplitter in extremelyhumid environments.

** Valid for room temperature and thermoelectrically cooled versions.


The next table lists the spectral ranges of compatible beamsplitter-detector combinations.

Light Range Beamsplitter Detector Spectral Range (cm-1) Source

visible quartz PbSe 13,000 - 2,800* Ever-Glo, white lightSi† 25,000 - 8,600 White light

CaF2 PbSe 13,000 - 2,000* Ever-Glo, white lightSi† 14,500 - 8,600 White light

near-IR quartz MCT-A‡ 11,700 - 2,800* Ever-Glo, white lightMCT-B‡ 11,700 - 2,800* Ever-Glo, white lightInSb‡,§ 11,500 - 2,800* Ever-Glo, white lightPbSe 13,000 - 2,800* Ever-Glo, white lightPbS TEC (with SabIR) 10,000 - 4,200* Ever-Glo, white lightInGaAs 12,000 - 3,800 Ever-Glo, white light

CaF2 MCT-A‡ 11,700 - 1,200* Ever-Glo, white lightMCT-B‡ 11,700 - 1,200* Ever-Glo, white lightInSb‡,§ 11,500 - 1,850* Ever-Glo, white lightPbSe 13,000 - 2,000* Ever-Glo, white lightPbS TEC (with SabIR) 10,000 - 4,200* Ever-Glo, white lightInGaAs 12,000 - 3,800 Ever-Glo, white light

XT-KBr MCT-A ‡ 11,000 - 600* Ever-Glo, white lightMCT-B‡ 11,000 - 400* Ever-Glo, white lightInSb‡,§ 11,000 - 1,850* Ever-Glo, white lightPbSe 11,000 - 2,000* Ever-Glo, white lightDTGS-KBr 11,000 - 375* Ever-Glo, white lightDTGS TEC 11,000 - 375* Ever-Glo, white lightInGaAs 12,000 - 3,800 Ever-Glo, white light

Continued on next page...

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Light Range Beamsplitter Detector Spectral Range (cm-1) Source

mid-IR KBr DTGS-KBr 7,400 - 350 Ever-GloMCT-A‡ 7,400 - 600 Ever-GloMCT-B‡ 7,400 - 400 Ever-GloDTGS TEC 7,100 - 350 Ever-GloDTGS-CsI 6,400 - 350 Ever-Glo

CsI¶ DTGS-CsI 6,400 - 200 Ever-GloMCT-A‡ 6,400 - 600 Ever-GloMCT-B‡ 6,400 - 400 Ever-Glo

ZnSe DTGS-KBr 4,000 - 650 Ever-GloMCT-A‡ 4,000 - 650 Ever-GloMCT-B‡ 4,000 - 650 Ever-GloDTGS TEC 4,000 - 650 Ever-GloDTGS-CsI 4,000 - 650 Ever-Glo

far-IR Solid-Substrate DTGS-PE 700 - 50 Ever-GloSi bolometer 700 - 20 Ever-Glo

Notes:* This spectral range reflects the combination of the ranges of the Ever-Glo and white light sources, as well as the limits of the

beamsplitter-detector combination. The range achieved using one of these sources will not be as broad as the total range shown.† Si detectors can be used only with a white light (tungsten-halogen) source.‡ These detectors must be cooled with liquid nitrogen before use.§ InSb detectors will not produce a signal under intense light. During installation and alignment, start with the smallest aperture setting.¶ CsI beamsplitters are extremely hygroscopic (sensitive to moisture).

Optimizingthe performanceof your detector

Nexus 870 detectors can be optimized to produce a more linearresponse and greater photometric accuracy, or to increase thesignal-to-noise ratio. You can achieve these improvements inperformance by adjusting the amount of infrared energy that reachesthe detector.


Improving linearityand photometric accuracy

Some detectors (including PbSe, Si, MCT-A and InSb detectors) arehighly sensitive and can become saturated or produce a distorted(non-linear and photometrically inaccurate) signal if the light energyis not reduced before it reaches the detector element.

Look at the low-end region of a single-beam spectrum (below thelow-end cutoff); you should see a straight line very near 0. As a ruleof thumb, the distance from 0 to the baseline should be less than 1%of the spectrum’s maximum intensity value. If the detector issaturated, you will see false energy in the low-end region. Thebaseline might be far above zero.

Note The maximum intensity of a mid-IR single-beam spectrum istypically found near 2,000 cm-1. ▲

The distorted signal may cause problems with photometric accuracy.For good quantitative data, the sample and backgroundinterferograms should be about the same size. Scattering samples andvery dense samples produce very small signals that can result indistorted quantitative data if the background signal is very large.

Check the low-end region or the background and sampleinterferograms. If you see a substantial difference in their size,photometric accuracy could be a problem.

To solve these problems, Nexus 870 spectrometers allow thefollowing options for modifying the infrared beam:

• Install a bandwidth-limiting filter.• Install an energy screen.• Adjust the aperture.

In Spectrometer Help Topics view “Setting up experiments” forinstructions on installing filters and energy screens.

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In some cases, system performance improves if you use a filter orscreen. The filter or screen that you should use for your applicationdepends on the samples being measured and other experimentalconditions. Try using various filters or screens to determine whichgive the best results for your application.

When to usebandwidth-limiting filters

Use bandwidth-limiting filters to improve the signal-to-noise ratio ofthe data and also prevent detector saturation by allowing only energyin your particular area of interest to pass to the detector element.

In Spectrometer Help Topics view “Installing an optical filter” in the“Setting up experiments” book for instructions on installing filters.

When to use energy screens Depending on the types of detectors you use, your system may includea set of four energy screens. These metal screens help prevent detectorsaturation and signal distortion by blocking out a portion of the energyat all frequencies of the infrared beam. If your experiments deal withinformation from a broad range of frequencies, these screens may bethe most effective means of reducing the light level.

The energy screens are labeled A, B, C and D. The following tableshows the percentage of the infrared energy that each screen passes.It also lists the detectors typically used with each screen, as a startingpoint for correcting linearity problems.

Screen % Transmitted* Detectors Typically Used With Screen

none 100 DTGS, MCT-B A 30 MCT-A B 10 PbSe, InSb, InGaAs C 3 D 1

* These are nominal values that may vary due to diffraction and detector variations.


To correct for photometric accuracy, you may need to add a “heavier”screen (one that transmits less infrared energy). With corrections forphotometric accuracy you will notice some reduction in the signal-to-noise ratio but will obtain more reliable quantitative data. Generally,the signal-to-noise ratio is reduced less than is the signal intensity.

In Spectrometer Help Topics view “Installing an energy screen” inthe “Setting up experiments” book for instructions on installingenergy screens.

What aperture size touse for your detector

The aperture is a variable-diameter opening that controls the angularsize of the infrared beam and, thus, the amount of radiation thatreaches the sample. Using an aperture has these advantages:

• It lets you use more sensitive detectors.

• It helps prevent infrared energy saturation, so the response of thedetector is more linear.

• It improves wavenumber accuracy and resolution by acting as apoint source of infrared radiation.

In general you will find that the larger the aperture, the better is thesignal-to-noise ratio of the collected data. The smaller the aperture,the better the stability and accuracy will be. Small apertures areneeded for high-resolution experiments.

DTGS detectors can accommodate most of the energy from thesource, which means you should use a large aperture size. Detectorsthat require cooling with liquid nitrogen are very sensitive andrequire a small aperture size or the use of an energy screen (see thepreceding section for more information).

Note On Nexus spectrometers, the setting of the Aperture parameterdetermines the area of the aperture opening. Doubling the settingapproximately doubles the area. A setting of 100 gives a nominalaperture diameter of 8 mm and an approximate area of 0.50 cm2. ▲

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The following table lists recommended aperture settings for differentdetectors with the appropriate energy screen installed. (See thepreceding section for information on the correct energy screen to usefor each detector type.) The settings in the table are based on thephysical size of the detector elements and maximize the amount ofinfrared energy that reaches the sample. To correct linearity andphotometric accuracy problems, you can reduce the setting, but youwill pay a price in terms of the signal-to-noise ratio.

Detector Aperture Setting

DTGS 100

MCT-A, MCT-B, InSb, PbSe, Si, InGaAs 32

? In OMNIC Help Topics find “aperture” in the Index and go to“Setting the aperture size” for information on changing the aperturesetting.

How to improve thesignal-to-noise ratio

If you primarily analyze qualitative data, you may wish to optimizethe system for a better signal-to-noise ratio. This can be particularlyimportant when you are working with scattering samples andsamples that absorb more infrared energy. These samples producesmaller signals that can be “lost” in the noise.

There are several ways to improve the signal-to-noise ratio. The mostcommonly used method is to increase the number of scans. This bothreduces the noise level and makes small absorptions easier todistinguish. You can also improve the ratio by reducing theresolution (using a larger Resolution setting).


Another method is to use an energy screen that transmits more light(or no screen at all). In this case, the resulting spectrum might bedistorted and accuracy and stability could be reduced. Checking thesingle-beam baseline in the region below the low-end cutoff willgive you a rough idea of how much distortion is occurring. If thedistance from the baseline to 0 is more than 15% of the spectrum’smaximum intensity value, you may have difficulty reproducing theresults.

Note If the distance from the baseline to 0 is greater than 20% of thespectrum’s maximum intensity value, your detector electronics maybe overloaded. Contact Nicolet Customer Support for assistance. ▲

In Spectrometer Help Topics view “Setting up experiments” forinstructions on installing filters and energy screens.

How to improvethe resolution

If you want to achieve higher resolution, you may need to use a smalleraperture setting and an energy screen that transmits more light (or noscreen at all). Your spectroscopy software will automatically changethe aperture setting if a smaller beam size is required. Be aware that thesmaller beam size will reduce the signal-to-noise ratio.

? In OMNIC Help Topics find “aperture” in the Index and go to“Setting the aperture size” for information on changing the aperturesetting.

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How to collectdata in the visible

spectral range

The ability of the spectrometer to collect data is affected by thedetector-beamsplitter combination and any energy screens or opticalfilters that are installed in the spectrometer. For example, if you use anoptional quartz beamsplitter, a silicon detector and a white-lightsource, the sampling range is extended to 25,000 cm-1.

Since silicon detectors are very sensitive, you will also need to installan energy screen or bandwidth-limiting filter to prevent the detectorfrom being saturated during the experiment. The following table listsa variety of spectral bands in the extended spectral range and lists thefilter or energy screen that should be used to obtain data in eachrange. It also lists typical aperture and gain settings for experimentsin each range.

Spectral Range Filter or Screen Aperture Gain

16,000 - 9,000 cm-1 red filter 32 1

16,000 - 9,000 cm-1 energy screen A 32 1

23,000 - 16,000 cm-1 broad-band blue filter 100 8

26,000 - 21,000 cm-1 narrow-band blue filter 100 8

You can use these filters and settings as a starting point and varythem as required by your experimental conditions. To set theaperture and gain, set the Aperture and Gain parameters on theBench tab in the Experiment Setup dialog box.

In Spectrometer Help Topics view “Installing an optical filter” in the“Setting up experiments” book for instructions on installing filters.


How to collectdata in the extended

spectral range

With OMNIC SST, the true spectral sampling range of yourspectrometer has been extended to 31,596 cm-1. You can make use ofthis range by setting Sample Spacing on the Advanced tab of theExperiment Setup dialog box to 0.5 whenever you specify a spectralrange (on the Bench tab of the Experiment Setup dialog box) thatexceeds 15,798 cm-1. When you use a sample spacing of one-half, fourdata points are collected during one laser period. (A setting of 1collects data twice, a setting of 2 collects data once, and a setting of 4collects data once for every two laser periods.)

Using a higher setting of Sample Spacing results in fewer collecteddata points, which allows you to use a faster scan velocity. With thisincrease in velocity, less time is required for data collection.

Note In step-scan experiments, you can use the sample spacing settingalone to shorten collection time. ▲

There are some constraints on using sample spacing to shorten datacollection time and still collect valid data. For example, the SampleSpacing parameter determines the nominal free (also known asnonaliased or nonambiguous) spectral range that you can reliablystudy, due to the Nyquist, or Sampling, theorem. The Nyquist theoremstates that at least two data points must be collected per period if youwish to reproduce the waveform accurately from discrete sampling.

Since a 15798 cm-1 frequency laser is used to trigger data collection,sample spacing limits the free spectral range for your interferogramas follows.

Sample Spacing Nominal Free Spectral Range

0.5 31,596 to 0 cm-1

1 15,798 to 0 cm-1

2 7,899 to 0 cm-1

4 3,949 to 0 cm-1

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If you allow energy from outside the free spectral range to reach thedetector, you will find that it corrupts your data with false energy. Toprevent this corruption, use an optical filter to prevent the unwantedenergy from reaching the detector and use an appropriatebeamsplitter-detector combination.

As an example, OMNIC uses a sample spacing of 2 for allexperiments where the data is collected in the region below7899 cm-1. You can run these experiments using the standardDTGS/KBr detector-beamsplitter combination, since thiscombination passes no energy above 7899 cm-1. No additionaloptical filters are required in this case.

However, if you are studying only data below 3940 cm-1, you canuse the sample spacing setting (along with the Velocity parameter) tocut the data collection time in half with little or no effect on thesignal-to-noise ratio. For these experiments you would set SampleSpacing to 4 and prevent energy above 3940 cm-1 from reaching thedetector.

? In OMNIC Help Topics find “sample spacing” in the Index and go to“Specifying the sample spacing” for more information about SampleSpacing.

There are several ways to prevent unwanted energy from reaching thedetector. The most common is to install a 3940 cm-1 low-pass opticalfilter in the beam path. In Spectrometer Help Topics view “Installingan optical filter” in the “Setting up experiments” book for instructionson installing filters.

As an alternative, you could install a band-pass filter (centeredaround your particular region of interest). If you choose a band-passfilter for use with a sample spacing of 4, make sure the upper limit ofthe filter is 3940 cm-1 or lower. No filtering would be required forexperiments that pass no energy above 3940 cm-1 to the detector.

Note If you do not have a 3940 cm-1 or 1900 cm-1 low-pass filter, you canorder one from Nicolet. ▲


Scan velocities To allow you to collect data faster, OMNIC SST and your Nexus 870spectrometer support increased linear scan velocities, up to 8.2277 cm/s.These higher velocities are useful for experiments where the sample islikely to change over time. The highest of these velocities will be usedwhen you perform rapid-scan experiments using OMNIC Series.

While a wide range of moving mirror velocities are available on theNexus 870, some velocity settings cannot be used for collecting dataat certain combinations of spectral range and resolution. Thefollowing tables show which velocity settings (in cm/s) are availablefor different resolution settings (in wavenumbers) under the specifiedconditions. A check mark (✓) indicates that the setting is available; adash (—) indicates that the setting is not available.

Sample spacing is set to 4 or 2, or the upper limit of the spectral range is less than or equal to7899 wavenumbers:

Resolution J

Velocity L

0.125 0.25 0.5 1.0 2.0 4.0 8.0 16.0 32.0

0.0158 -5.6961

✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓

6.3290 — — ✓ ✓ ✓ ✓ ✓ ✓ ✓

6.9619 — — — — ✓ ✓ ✓ ✓ ✓

7.5948 — — ✓ ✓ ✓ ✓ ✓ ✓ ✓

8.2277 — — — — — ✓ ✓ ✓ ✓

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Sample spacing is set to 1, or the upper limit of the spectral range is within the range 7900 to15798 wavenumbers:

Resolution J

Velocity L

0.125 0.25 0.5 1.0 2.0 4.0 8.0 16.0 32.0

0.0158 -2.5317

✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓

3.1647 -3.7974

— — — ✓ ✓ ✓ ✓ ✓ ✓

4.4303 — — — — — — ✓ ✓ ✓

4.7468 -5.6961

— — — — — — — ✓ ✓

6.3290 — — — — — — — — ✓

6.9619 -8.2277

— — — — — — — — —

Sample spacing is set to 0.5, or the upper limit of the spectral range is within the range 15799 to31596 wavenumbers:

Resolution J

Velocity L

0.125 0.25 0.5 1.0 2.0 4.0 8.0 16.0 32.0

0.0158 -1.2659

✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓

1.8988 — — — — — ✓ ✓ ✓ ✓

2.5317 — — — — — — — — ✓

3.1647 -8.2277

— — — — — — — — —


To specify the velocity and spectral range, set Velocity and SpectralRange on the Bench tab of the Experiment Setup dialog box. Tospecify the resolution, set Resolution on the Bench tab.

Important When you switch to a different detector or beamsplitter, OMNICautomatically resets the default spectral range in the ExperimentSetup dialog box. Be sure to check the range and set the velocity to avalue that is appropriate (see the limitations described above). ▲

Note When collecting rapid scan data with a sampling interval of less than0.04 second, do not interact with the computer (with the mouse orkeyboard) until the collection is finished; otherwise, Windows mayinterrupt the collection. The current sampling interval is shown on theCollect tab of the Series Setup dialog box and is calculated from theresolution, mirror velocity and number of scans per spectrum orinterferogram. ▲

Slow scan Slow scan allows the moving mirror to be precisely controlled at verylow velocities. Among other applications, this is particularly useful forphotoacoustic experiments. Slow scan is an experimental techniqueand we invite you to explore new applications.

As with other linear applications, data in slow-scan applications iscollected continuously, as the moving mirror travels at a constantvelocity within the interferometer. Each light wave is modulatedindividually, with the modulation frequency equal to the mirrorvelocity multiplied by the wavelength of the light wave.

Due to the low velocities, you will notice a decrease in thesignal-to-noise ratio in slow-scan experiments. You can improve itby increasing the number of scans.

No special hardware setup is required for slow-scan experiments.Nearly any hardware you use for other linear scan experiments canbe used for slow-scan experiments. Some experiments that areusually run in step-scan mode (such as photoacoustic spectroscopy)can also be run using slow-scan.

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Note Reduce the aperture setting or use an appropriate filter or screenwhen running slow-scan experiments to prevent saturating theDTGS, photoacoustic or other thermal detector. If you are not usinga filter or energy screen, an aperture setting of 2 is common for slow-scan experiments. ▲

View “What is slow scan?” in the “Welcome to Nexus 870!” unit ofthe Spectrometer Tour (available through Getting Started) for anoverview of slow-scan applications.

A note about vibrations All slow-scan experiments are prone to disruption from vibrations.Should your experiment be disrupted, the Nexus 870 spectrometer willautomatically recover. You do not need to restart the data collection.

If your experiment is disrupted by vibration, you can expect to hear aclicking sound as the moving mirror is repositioned. This may take aminute or two. Once the mirror is repositioned, data collection willresume from the last valid scan.

Runningslow-scan experiments

The slow-scan capabilities are available on the Bench tab of theExperiment Setup dialog box.

Use the Velocity setting on the Bench tab to access slow scan.Selecting any of the velocities below 0.1581 cm/s puts thespectrometer in slow-scan mode. Use Collect Sample and CollectBackground in the Collect menu to start your slow-scan experiments.

When you finish running slow-scan experiments, use ExperimentSetup to change the Velocity setting to 0.6329 cm/s or higher. This isespecially important if your next experiment will be a step-scanexperiment. The spectrometer cannot automatically shift fromslow-scan mode to step-scan mode.


Using the SST Software

The SST menu in OMNIC gives you access to the SST experimentsthat are available on your system. This chapter provides specificinformation for using the software to perform each experiment.

View “What is SST?” in the “Welcome to Nexus 870!” unit of theSpectrometer Tour (available through Getting Started) for an overviewof the SST software.

Starting theSST software

Follow these steps to start the SST software:

1. Start OMNIC.

Double-click the OMNIC E.S.P. shortcut on the Windows desktop.

Depending on how the program has been configured, dialogboxes may appear asking for a user name and password. Typeyour user name if requested, and then choose OK. Enter apassword if required.

The OMNIC window appears.

2. Set the experiment parameters.

You can do this in one step by selecting an experiment from theExperiment drop-down list box near the top of the window.

You can also use Experiment Setup in the Collect menu to open anexperiment or set the parameters individually. These parametersinclude File Handling and Background Handling on the Collect taband Sample Compartment, Detector, Beamsplitter, Source andAperture on the Bench tab of the Experiment Setup dialog box.

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3. Click SST in the menu bar to display the SST menucommands.

On-line Help for SST You can access on-line Help for the SST software by choosing SSTHelp from the SST menu. Also, if you press the F1 function keywhile you are in any SST dialog box or window or while any SSTmenu command is highlighted, the on-line Help information for thatitem appears.

Collectingdata with SST

After you have started the SST software, you can use the commandsin the SST menu to collect sample and background data. Followthese steps:

1. Choose the technique you wish to use from the SST menu.

The menu lists the experiments that are available for yourspectrometer.

Note Time-Resolved Step Scan experiments are available if you purchasedthe optional OMNIC SST with TRS Experiments software package. ▲

2. When the setup dialog box for the SST technique appears, setthe parameters for your experiment.

Note If you change the spectral resolution, points before peak, or samplespacing parameters using one of the SST setup screens, it changesthat parameter for all SST and standard OMNIC data collectiontechniques. ▲

3. When the software is set up for your experiment, choose OK.

You are returned to OMNIC.


4. Use the commands in the SST menu to collect yourbackground or sample data.

Ratioing spectra The Ratio Spectra command in the SST menu allows you to performspectral division, ratioing any one spectrum or a group of three ormore spectra against a common background spectrum. Thebackground spectrum must be stored on a disk. You may also ratiotwo active spectra against each other.

Note Whenever you ratio spectra, all of the spectra you select must be inthe same final format. For example, you cannot ratio an absorbancespectrum against a transmittance spectrum. ▲

Ratioing spectraagainst a common

stored background

Follow these steps to generate a ratioed spectrum from a storedbackground:

1. Open any spectrum.

If you wish to ratio a group of spectra, open all of the spectrainto one spectral window.

2. Select the spectra you wish to ratio.

3. Choose Ratio Spectra from the SST menu.

The Ratio Spectra dialog box appears.

4. Select the spectrum to be used as the denominator.

Use the Browse button to locate and select a backgroundspectrum that you previously saved on a disk.

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5. Select the destination for the ratioed spectra.

6. Choose OK to generate the ratioed spectrum.

The results of the ratio operation appear in the window youselected.

Note Choose Cancel to exit the dialog box without ratioing the spectra. ▲

The special case ofratioing only two spectra

When you use the Ratio Spectra command with only two single-beam spectra selected, the command operates a bit differently. Itgenerates a ratioed spectrum from those spectra. In this case, you donot have the opportunity to select a stored background spectrum. Ifyou need to ratio only two spectra against a stored background, ratioeach of them separately.

Follow these steps to generate a ratioed spectrum from two selectedspectra:

1. Open and select the two single-beam spectra you wish toratio.

2. Choose Ratio Spectra from the SST menu.

The Ratio Spectra dialog box appears. Here is an example:


3. If the spectra are not correctly positioned as numerator anddenominator, click the Swap button at the right.

4. Choose OK to generate the ratioed spectrum.

Choose Cancel to exit the dialog box without ratioing the spectra.

The results of the ratio operation appear in the spectral window.

Using SST phasearray operations

Phase array operations allow you to reprocess (using the commandsin the OMNIC Process menu) spectra collected using PM step-scan,PEM and other experimental techniques that generate two or morespectra from the same scan. You can also use them to view andmanipulate phase correction arrays for other spectra.

What is a phase array? A phase array is a frequency-dependent list (or spectrum) of phaseangles calculated from the Fourier transform of an interferogramtruncated about the central peak maximum. Each phase angle in thearray is defined by the following equation:

φ i = arctan(I i / Ri )

where Ii and Ri are the imaginary and real points from the Fouriertransform at frequency i.

The phase array is used to correct the full-resolution single-beamspectrum for phase shifts caused by optical differences in thebeamsplitter substrate and the compensator plates and for theprobability that the central peak maximum point is not at exactly thezero-path-difference (ZPD) point.

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What is phase correction? Phase correction is one of several operations performed on the datacollected by the detector. During the conversion of an interferogramto a spectrum that can be analyzed, the apodization and zero fillingoperations that you selected using Experiment Setup, the Fouriertransform operation, and the phase correction operation areperformed.

The phase correction is calculated using the following formula:

Xi = Ri cosφ i + Ii sinφ i

where Ri and Ii are the real and imaginary points from the Fouriertransform of the entire interferogram at frequency i, Øi is a phaseangle from the phase array (interpolated, if necessary), and Xi is thesingle-beam spectrum.

In some experiments, such as PEM step scan, TRS step scan and PEM,more than one interferogram is collected during a single scan. Toobtain valid data from these experiments, a single phase correctionarray must be used for all the interferograms collected during the scan.

When you use the Collect Sample command in the SST menu, this ishandled automatically by the OMNIC SST software. When youreprocess the data, the OMNIC software must be directed (using thePhase Array Operations command in the SST menu) to use the samephase correction array for all of the interferograms. If you do notdirect OMNIC to use a stored phase array, a new phase array will becalculated from each interferogram.

Phase array operations The Phase Array Operations command in the SST menu lets youcalculate, store and use a stored phase array for correcting anyspectrum. You can also examine and manipulate the phase arrayused for the correction. This is useful when you need to applydifferent Y-axis constraints to the phase array.


Calculating a phase array Follow these steps to calculate a phase array:

1. Save the interferograms when you collect the data.

There are two options for saving interferograms.

You can turn on Save Interferograms before beginning datacollection. This option is in the File Handling box on the Collecttab in the Experiment Setup dialog box.

You can select Interferogram as your final format. The FinalFormat parameter is on the Collect tab in the Experiment Setupdialog box.

2. Open and select the interferogram.

If you selected Interferogram as your final format:

Use Open in the File menu to display the interferogram in aspectral window. The interferogram is selected automatically.

If you chose to save the interferograms with your spectrum:

Use Open in the File menu to display the spectrum in a spectralwindow.

Choose Reprocess from the Process menu.

Select Interferogram from the Final Format drop-down list box.

Choose OK. The interferogram appears in a spectral window.

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3. Choose Phase Array Operations from the SST menu.

The Phase Array Operations dialog box appears.

4. Choose Calculate Phase Array.

5. Configure OMNIC to use the stored phase array.

Turn on the Use Stored Phase Array check box and then chooseOK.

OMNIC will use that stored phase array to process all subsequentinterferograms until you turn the check box off or store anotherphase array.


Viewing a phase array You must calculate the phase array before you can view it. Followthese steps:



2. Choose View Phase Array.

The phase array appears in the active spectral window. You canmanipulate it using the commands in the Process menu. You canthen store the modified phase array and use it to generate spectra.

Refer to the OMNIC Help system if you are unfamiliar with theProcess menu commands.

Storing a phase array You must calculate and view the phase array before you can store it.Follow these steps:

1. Select the phase array.



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3. Choose Store Phase Array.

The phase array is stored in memory, from which you can use itto process interferograms.

4. Configure OMNIC to use the stored phase array.

Turn on the Use Stored Phase Array check box and then chooseOK.

OMNIC will use that stored phase array to process all subsequentinterferograms until you turn the check box off or store anotherphase array.

Saving a phase array You must calculate and view the phase array before you can save it.Follow these steps:

1. Select the phase array.

2. Save the phase array.

Use the Save As command in the File menu.

You will be prompted for a filename and directory path. Refer tothe OMNIC Help system and your Windows documentation ifyou are unfamiliar with naming and saving files.

The phase array will be saved as a standard OMNIC spectral datafile. You can open it using any program that can read OMNICfiles.


Accessories

This chapter briefly describes the types of sampling and systemaccessories that are available for your spectrometer. Completedescriptions and operating instructions are included with theaccessories.

Smart Accessories In addition to traditional accessories, a variety of Smart Accessoriesare available for your spectrometer. The Nexus system uses E.S.P.technology to identify each Smart Accessory as soon as it is installedand set the software parameters for data collection. Also, a series ofspectral quality checks are performed to ensure that the accessory isinstalled and operating correctly.

In Spectrometer Help Topics view “Installing a Smart accessory” inthe “Installing optional hardware” book for instructions on installingSmart Accessories.

Nexus Smart ARK – This is a horizontal ATR accessory withhigh stability, complete purge capabilities, tool-free alignment andhigh performance specifications. It includes integral purge tubes thatseal the accessory from the atmosphere, and an aluminum, cast bodyfor exceptional stability.

Nexus Smart Collector – Diffuse reflection enables analysis ofhighly light-scattering solids that are difficult to analyze usingtransmission techniques. This method is also useful when thesample, usually a powder, must be analyzed without modification.

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Nicolet Near-IR FiberPort – This accessory is optimized for near-IR sampling. The probe combines input and collection fibers in aunique sampling tip. In reflectance mode, solids and light-scatteringliquids can be analyzed through direct contact. Transflectance mode isused for transparent liquids. This accessory is useful for thenondestructive study of polymers, pharmaceuticals, foods, fabrics andchemicals, as well as biological and environmental samples. Theaccessory uses an optimized lead sulfide detector.

Nicolet Mid-IR FiberPort – This high-throughput accessory letsyou analyze liquids remotely. The needle probe can reach “hard toget” samples, such as liquids in micro containers, hazardousenvironments or remote locations. The FiberPort is a unique opticalinterface that transfers IR energy from the spectrometer to the fiberoptic cables and probes. A complete line of fiber optic probes isavailable for sampling a wide range of sample types.

Nicolet Smart MIRacle – This a single-reflection horizontal ATRaccessory with exceptional throughput and sensitivity. It can useseveral crystal types and has a micrometer screw for precise controlof applied pressure.

Nicolet Smart DuraSamplIR – This single-reflection horizontalATR accessory has a viewing feature that makes it easy to positionthe sample and monitor the applied pressure. The accessory is idealfor small samples and can be used to measure liquids, powders andpliable solids.

Nicolet OMNI-Sampler – This single-reflection ATR accessoryfeatures a spherical crystal that lets you measure a wide variety ofsample types. The unique tower design automatically applies theoptimum pressure while protecting the crystal. The accessory is idealfor analyzing very small samples or sample areas and provides highreproducibility.

Nicolet OMNI-Transmission – This easy-to-install transmissionaccessory lets you sample liquids, gases and solids using a widevariety of transmission cells and infrared cards.


Nicolet Near-IR UpDRIFT – This is a top-loading diffusereflection accessory designed for fast analysis of solids and powders.In many cases you can analyze samples directly from plastic or glasscontainers.

Nicolet Smart Golden Gate – This is a horizontal, single-reflectionATR accessory that features an extremely durable diamond crystal. Ithandles a wide range of sample types, including hard or brittlesolids, corrosive liquids and hard powders.

Avatar Single-Bounce HATR – This is a single-reflectionhorizontal ATR accessory that has a shorter pathlength and higherthroughput than traditional HATR accessory design. It is the bestchoice for routine analysis of strong infrared-absorbing samples.This is an economical choice for quality control or academicenvironments where routine analyses of neat solvents, aqueoussolutions, powders and film samples are required.

Avatar Multi-Bounce HATR – This is a multi-reflection horizontalATR accessory that has a shorter pathlength and higher throughputthan traditional HATR accessory design. It is the best choice forroutine analysis of strong infrared-absorbing samples. This accessoryis ideal for rapid quantitative and qualitative analyses, since samplepreparation is usually not necessary.

Avatar Diffuse Reflectance – The diffuse reflection technique letsyou analyze highly light-scattering solids that are difficult to analyzeusing transmission techniques. The technique is also useful when thesample, usually a powder, must be analyzed without modification.This accessory lets you analyze a wide variety of sample types andfeatures integral sample cups for convenient, fast sampling.

? In OMNIC Help Topics find “accessory” in the Index and go to“Specifying the accessory” for instructions on setting up and savingexperiments for custom accessories.

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Other samplingaccessories for

different applications

You can install many of these sampling accessories yourself. Afteryou install an accessory, you might have to align it. Instructions foraligning the spectrometer are included in the “Service andMaintenance” chapter of this manual. Instructions for aligning anaccessory are provided in the documentation that came with thataccessory.

Most accessories fit into the sample compartment, but some requireseparate housing and optics. Nicolet offers auxiliary experimentmodules, microscopes, gas chromatography interfaces andthermogravimetric analysis interfaces with the Nexus 870.

Some accessories have their own optics. The optional mirror opticsinside the spectrometer redirect the light beam from the internal lightsource through a port on the right side of the spectrometer. The beamthen travels into the accessory’s optics.

Some of the accessories fit into the sample compartment and requirethat you remove the standard Snap-In baseplate before installing theaccessory. For information on using Snap-In baseplates, view“Removing the Snap-In baseplate” in “Setting up experiments” inSpectrometer Help Topics.

Call Nicolet if you are interested in ordering any of the followingsampling accessories.

Note Additional Snap-In sample compartment baseplates are available foruse with each accessory to make changing accessories easier. ▲

Automatic sample wheel – This accessory holds multiple samplesand rotates them into the beam path for data collection. The samplewheel is commonly used to measure multiple polymer or pressed-powder samples automatically.


Auxiliary experiment module (AEM) – The AEM provides youwith an additional sample compartment. You can position it on theright or left side of the spectrometer. With an AEM installed, youcan run routine analyses with the spectrometer and quickly switchbeam paths to the AEM to collect data from other samples withoutremoving accessories from the main sample compartment. Anyaccessory or detector that can be installed in the spectrometer can beinstalled in the AEM. The AEM has two detector locations.

Continuµm, InspectIR and Advantage infrared microscopes –Nicolet offers microscopes that attach directly to either side of thespectrometer. Microscopes can also be installed between thespectrometer and other accessory modules. The microscopes providefast, nondestructive microanalysis with minimal sample preparationand alignment. The beam path is switched from the spectrometer tothe microscope module through the OMNIC software.

Custom accessory baseplate – You can use this Smart baseplate tomount an accessory you have built or purchased from anothermanufacturer. When you install the accessory and baseplate in thesample compartment, the system automatically selects the CustomAccessory experiment (or allows you to select from the experimentsyou have saved for the baseplate).

Detector interface kit – A variety of accessories (that werespecifically designed for Nexus 870 spectrometers) contain detectorsthat are automatically recognized by your spectrometer. The detectorinterface accessory allows your spectrometer and OMNIC softwareto recognize other detectors, including non-Nicolet detectors.

Gas cells – A variety of short- and long-pathlength gas cells areavailable. Cells include built-in transfer optics that fit into yourspectrometer or AEM sample compartment. The cells are suitable foruse in both ambient and elevated temperature conditions. Gas cellheating, transfer optics purge, gas manifold, and sample windowoptions are available to accommodate a variety of sample gases andsampling conditions.

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GC interface – This interface attaches to the right side of thespectrometer and must be connected to a gas chromatograph (GC).You can then analyze IR spectra from GC experiments using theOMNIC Series software.

Gemini – By combining two sampling technologies—horizontalattenuated total reflection (HATR) and diffuse reflection—thisaccessory lets you analyze a broad range of sample types. TheGemini is baseplate-mounted for high stability, and no accessoryrealignment is necessary when you switch sampling heads. Integralpurge tubes seal the accessory from the atmosphere.

PAC 300 Photoacoustic E.S.P. – Photoacoustic spectroscopy (PAS)is a powerful technique for the nondestructive spectroscopic analysisof solid samples of all types. PAS is particularly applicable topowders (including dark, highly absorbant samples), polymer pellets,beads, and sheets and films. The PAC 300 Photoacoustic E.S.P.accessory is fully integrated with the spectrometer and computer. Itautomatically selects an OMNIC experiment, draws power rightfrom the spectrometer and includes an on-line tutorial.

PEM kits – A variety of PEM (photoelastic modulator) externalhardware kits include a lock-in amplifier, high-pass filter, the PEM,transmission and grazing angle sample holders, a polarizer, transferand focusing optics, and optical filters. These kits contain all thehardware needed to perform VCD (vibrational circular dichroism)and PM-IRRAS (polarization modulation infrared reflectionabsorption spectroscopy) experiments. The optional OMNIC SSTwith PEM Experiments software package is required for theseexperiments.

Remote Start accessory – This accessory adds external triggercapability to your spectrometer. With a press of the Start switch, youcan control the start of data collection or coordinate the start of anexternal experiment.


Sample shuttle – A sample shuttle lets you collect backgroundspectra without removing the sample from the sample compartment.The shuttle automatically moves the sample out of the beam pathbefore background collection begins. Since the sample compartmentcover is not opened, the system purge is maintained.

Specular reflection – Specular reflection provides a nondestructivemethod for measuring surface coatings without sample preparation.It can be used to analyze surface-treated metals, paints,semiconductors, and resin and polymer coatings. Specular reflectionaccessories can be installed in the spectrometer sample compartmentor AEM.

TGA interface – This interface is equipped with a built-in,temperature-controlled flow cell and must be connected to athermogravimetric analysis (TGA) furnace. You can analyze theevolved gases from TGA experiments using the OMNIC Seriessoftware. The TGA interface is usually mounted in the samplecompartment of an AEM.

Transmission E.S.P. – Transmission is the oldest and most efficientsampling technique in FT-IR spectroscopy and can be used forsampling liquids, gases or solids. A variety of cells and sampleholders are available for transmission analysis. All can be mountedin the spectrometer sample compartment or an auxiliary experimentmodule.

TRS kits – Each TRS (time-resolved step-scan) kit includes a fasttransient data acquisition card, a high-speed photovoltaic MCTdetector and the OMNIC SST with TRS experiments softwarepackage needed to perform a variety of time-resolved experiments.Time-resolved measurements to 10 nanoseconds are possible.

Validation wheel – The validation wheel is used with Nicolet’sSystem Validation software to validate the performance of thespectrometer. The wheel automatically moves standard samples intothe beam path at the appropriate times during the validation procedure.

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System accessories Some system accessories are installed by Nicolet. Call Nicolet if youare interested in ordering any of the following accessories.

Power line conditioner – Power line conditioners protect yourspectrometer and other accessories from damage or malfunction dueto voltage dropouts, transient spikes, frequency shifts or otherdisturbances in your electrical service.

Uninterruptable power supply – An uninterruptable power supplyreduces the chance of a system shutdown if power is lost elsewherein the building.

Pure air generator – Nicolet offers a complete dry-air generationsystem. It includes an air compressor, a dryer, prefilters, a finalfilter/moisture indicator, and flow controls. If you have difficultycontrolling moisture in your laboratory, the pure air generatorprovides additional protection for the hygroscopic elements of yourspectrometer. This accessory is also useful if your laboratoryenvironment is contaminated with volatile solvents, oil or otherreactive materials.

Purge gas generator – If you do not have in-house facilities tosupply compressed air or nitrogen for system purge, Nicolet offersseveral purge gas generators.

Smart Purge Kit – This kit adds enhanced purging capability toyour spectrometer. When you open the sample compartment cover orits sliding door, Smart Purge automatically increases the purge gasflow rate for a short time. This keeps water vapor, carbon dioxideand other unwanted gases out of the spectrometer while you installor remove a sample. You can then collect spectra without waiting forproper purge to be restored.


How to cablean accessory

When you install an accessory in the sample compartment, you mayneed to connect one or more cables from the accessory to connectorson the rear wall of the compartment. You may also need to attachcables from other peripherals (such as computers, custom controllersor power supplies) to the accessory or from the accessory to the rearpanel of the spectrometer. The instructions that came with theaccessory should contain specific information on connecting thataccessory.

See the illustrations in the next sections for the locations of theconnectors.

Pass-through connectors Your spectrometer may be equipped with pass-through connectorsfor use with special accessories. These connectors allow you to makeaccessory cable connections through the spectrometer. Thiseliminates the need to run cables through the seal on the samplecompartment cover or out the top of the sample compartment.

Warning Improper or unsafe cabling can cause damage to your accessory andmay create a safety hazard. Only qualified persons should cable acustom accessory using these connectors. Nicolet is not responsiblefor damage or injury resulting from improper or unsafe cabling. ▲

To use the pass-through connectors, connect the accessory inside thesample compartment and connect the external power orcommunications peripheral to the corresponding pass-throughconnector on the rear panel of the spectrometer.

See the next sections for details.

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Connectors inside thesample compartment

The following illustration shows the locations of the electricalconnectors inside the sample compartment:

Detector/Motors

Auxiliary

PurgeOut

Optional pass-through connectorfor communication or other signal

Accessory connector for detectorsignal or accessory control and power

Detector/Motors – If you have a photoacoustic or other accessorythat has a detector or motor located in the spectrometer samplecompartment, connect the cable from the detector or motor to thisstandard connector. This is not a pass-through connector. See“Detector/Motors connector” for information on using this connectorto connect custom hardware.

Auxiliary – Six pins on this optional connector can be used forpassing DC power input or other signals from the Auxiliary 1 andAuxiliary 2 connectors on the rear panel to an accessory. Forexample, the automatic sample wheel and the ProfilIR accessory getDC power through this connector when the DC power output of anAC-to-DC converter is attached to the Auxiliary 1 connector on therear panel. See “Using connectors for custom accessories” forinformation on which pins are available for use.


Connectors on the rear panel The illustration below shows the optional connectors on the rearpanel that you can use to pass signals to and from the samplecompartment.

Pass-through connector(for DC power input

or other signal)

Pass-through connector(for communication

or other signal)

Auxiliary 1 – This connector passes power or other signals for theaccessory to three pins on the Auxiliary connector inside the samplecompartment. This connector could be used, for example, to attachthe DC output of an AC-to-DC converter to provide DC power to anaccessory in the sample compartment.

Auxiliary 2 – This connector passes signals to three pins on theAuxiliary connector inside the sample compartment. This connectorcould be used, for example, to allow an accessory in the samplecompartment to be controlled through your computer’s serial(RS-232C) port.

See the next section for information on which pins are available foruse.

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Using the pass-throughconnectors for

custom accessories

By connecting custom cables that use the pins on the pass-throughconnectors, you can provide power and communication or othersignals for your custom accessories. The power and signals passthrough the spectrometer from the rear panel to the samplecompartment and vice versa. Make sure your use of the connectorscomplies with the voltage and current limitations given in thefollowing Warning.

Warning Improper or unsafe cabling can cause damage to your accessory andmay create a safety hazard. Only qualified persons should cable acustom accessory using these connectors. Do not pass signals thatexceed ±15 VDC through these connectors. You must also limit thecurrent to a maximum of 800 mA. Nicolet is not responsible fordamage or injury resulting from improper or unsafe cabling. ▲


The following diagram shows schematically which pins of theAuxiliary connector inside the sample compartment are connectedinternally to pins of the Auxiliary 1 and Auxiliary 2 connectors onthe rear panel. Since none of these connected pins are assigned bythe Nexus 870, they are available for use with custom accessories.

8 7 6 5 4 3 2 1

15 14 13 12 11 10 9

12

34

5

67

89

12

34

5

67

89

Auxiliary

(male)1

2 (female)

Sample CompartmentConnector

Rear PanelConnectors

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Detector/Motorsconnector

You can use the Detector/Motors connector on the rear wall of thesample compartment to connect your own detectors, accessorymotors and other custom hardware.

8 7 6 5 4 3 2 1

15 14 13 12 11 10 9

Detector/Motors

Make sure your use of the connector complies with the voltage andcurrent limitations given in the following Warning.

Warning Improper or unsafe cabling can cause damage to your accessory andmay create a safety hazard. Only qualified persons should connect acable to the Detector/Motors connector. Do not use this connector forsignals that exceed ±15 VDC. Limit the current to a maximum of800 mA. Nicolet is not responsible for damage or injury resultingfrom improper or unsafe cabling. ▲


The following table shows “pinout” information for theDetector/Motors connector. Use this information when designing acable to connect your custom hardware to the connector. Refer to thepreceding illustration for the locations of the numbered pins.

Pin Number Description

1 Do not use this pin.

2 Used by the sample shuttle motor (negative).

3 Positive 5 volts.

4 Analog ground.

5 Used by the sample compartment detector fornegative analog input.

6 Positive 12 volts analog.

7 Used by the sample compartment detector for digitalcommunication.

8 Positive 5 volts.

9 Used for sample compartment digital communication.

10 Used by the sample shuttle motor (positive).

11 Positive 12 volts.

12 Analog ground.

13 Used by the sample compartment detector for positiveanalog input.

14 Negative 12 volts analog.

15 Used by the sample compartment detector for digitalcommunication.

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Quick Answers to Your QuestionsAbout Using OMNIC

This chapter answers some common questions about using OMNIC.Each answer is followed by a reference telling you where to go formore information.

Collecting spectra How do I set the software for collecting spectra?

You can set the software in one step by selecting a stored experimentfrom the Experiment drop-down list box below the OMNIC windowmenu bar. To set the experiment parameters individually, useExperiment Setup in the Collect menu.

If you install a Smart Accessory, the system automatically sets thesoftware parameters (or a list of appropriate experiments is madeavailable for your selection), and you can begin collecting spectra.

Collecting a Spectrum (available through Learning OMNIC)...“Preparing the Software”

? In OMNIC Help Topics find “experiment” in the Index and go to“Selecting an experiment” or “Using Experiment Setup.”

? SST Help Topics in the SST menu

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How do I collect a spectrum?

Set the parameters as explained above and then choose CollectSample from the Collect menu. Depending on the parameter settings,you may need to install or remove the sample before choosingCollect Sample.

Collecting a Spectrum (available through Learning OMNIC)...“Collecting the Spectrum of a Sample”

? In OMNIC Help Topics find “spectrum” in the Index and go to“Collecting a sample spectrum” or “Collecting a backgroundspectrum.”

? SST Help Topics in the SST menu

How do I specify the Y-axis unit for collecting spectra?

Choose Experiment Setup from Collect menu and then set FinalFormat on the Collect tab.

You can change the format of a collected spectrum by usingAbsorbance, % Transmittance or Other Conversions in the Processmenu. See the question and answer in the next section for adescription of the available units.

Collecting a Spectrum (available through Learning OMNIC)...“Typical IR Transmission Spectrum”

? In OMNIC Help Topics find “units” in the Index and go to“Selecting the final format.”


What does gain do?

Gain amplifies the detector signal intensity, making it larger relativeto the level of electronic noise. This is helpful when the signal isweak, such as when you use some sampling accessories. You can letOMNIC automatically adjust the gain to maximize the signal bysetting the Gain parameter to Autogain. We recommend using thissetting to ensure the best spectral quality.

? In OMNIC Help Topics find “gain” in the Index and go to “Settingthe gain.”

When should I save interferograms with my spectra?

Save interferograms if you think you may want to restore the originaldata after it has been processed or if you want to keep an archive ofyour raw data.


? In OMNIC Help Topics find “saving, interferograms” in the Indexand go to “File handling.”

What does the Collect Sample window show?

The window displays the “live” spectrum as it is being collected plusa gauge indicating the progress of the collection, an indicatorshowing whether any problems have occurred and other informationabout the collection.

Collecting a Spectrum (available through Learning OMNIC)...“Collecting the Spectrum of a Sample”

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? In OMNIC Help Topics find “spectrum” in the Index and go to“Collecting a sample spectrum.”

How do I know my spectra are meeting quality standards?

OMNIC continuously monitors the quality of the data you collect,based on the parameters you set. The Quality tab in the ExperimentSetup dialog box contains parameters for specifying the spectralquality characteristics that you want checked when you collectspectra.

OMNIC offers four categories of spectral quality checks:

• Spectrum checks• Parameter checks• Background checks• Interferogram checks

When OMNIC performs a check and detects a problem, the CollectStatus indicator is displayed as a yellow circle or a red X. Click theindicator (or click the View Collect Status button at the end of datacollection) to see a summary of data collection problems encounteredduring the collection and other information about the collection.

When a collected spectrum passes all of the selected quality checks,the Collect Status indicator appears as a green check mark.

? In OMNIC Help Topics find “quality” in the Index and go to“Quality tab.”


Convertingspectra to other units

Which Y-axis unit should I use for a spectrum?

The most commonly used units are % transmittance and absorbance.Use % transmittance if you plan to compare the spectrum visuallywith published reference spectra. Use absorbance units forquantitative analysis measurements.

Kubelka-Munk units are useful for searching diffuse reflectancespectra against libraries of absorbance spectra.

Use photoacoustic units for spectra collected using a photoacousticaccessory.

Percent reflectance units are mathematically equivalent to %transmittance units, but using them for spectra collected using areflection technique serves to identify the technique.

Using log (1/R) units for spectra collected using a reflectiontechnique is useful for quantitative comparisons, since there is oftena linear relationship between the concentration of a component andits log (1/R) value.

Collecting a Spectrum (available through Learning OMNIC)...“Typical IR Transmission Spectrum”

? In the OMNIC Help Topics Index...

Find “absorbance” and go to “Converting spectra to absorbance.”

Find “transmittance (%)” and go to “Converting spectra to% transmittance.”

Find “Kubelka-Munk units” and go to “Kubelka-Munk units.”

Find “photoacoustic units” and go to “Photoacoustic units” topic.

Find “reflectance (%)” and go to “% Reflectance units.”

Find “log (1/R) units” and go to “Log (1/R) units.”

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Usingspectral libraries

How do I search a spectral library?

First prepare the spectrum (as explained below) and display or selectthe region you want searched. Then set up the search using LibrarySetup in the Analyze menu and start the search by clicking theSearch button in the Library Setup dialog box or by choosing Searchfrom the Analyze menu.

? In OMNIC Help Topics find “library” in the Index and go to“Setting up a library search” or “Searching a spectral library.”

How should I prepare my spectrum before searching it against aspectral library?

There are several corrections you can perform on a spectrum toobtain the best search results:

• If the baseline of the spectrum is sloped, curved or shiftedvertically, correct it using Baseline Correct in the Process menu.

? In OMNIC Help Topics find “baseline” in the Index and go to“Correcting a baseline manually.”

• If the spectrum has totally absorbing bands, eliminate them byusing Blank in the Process menu. Be careful not to blank regionsthat contain other important spectral information.

? In OMNIC Help Topics find “blanking spectral region” in theIndex and go to “Blanking a spectral region.”

You can also use the region tool to select a region of thespectrum that does not include any totally absorbing bands or usethe view finder to display the region before searching. (Thesemethods avoid the loss of spectral information that results fromblanking.)


? In OMNIC Help Topics find “spectral region” in the Index andgo to “Region tool” or “View finder.”

• If you collected the spectrum using specular or diffuse reflection,use Kramers-Kronig (dispersion) correction (available throughOther Corrections in the Process menu) to correct it fordispersion effects and then search it against a library ofabsorbance spectra.

? In OMNIC Help Topics find “Kramers-Kronig transformation”in the Index and go to “Kramers-Kronig (dispersion)transformation.”

• If you collected the spectrum using ATR (attenuated totalreflection), use ATR correction (available through OtherCorrections in the Process menu) to correct it for variation in thedepth of penetration and then search it against a library oftransmission spectra.

? In OMNIC Help Topics find “ATR correction” in the Index andgo to “ATR correction.”

• If the spectrum has water or carbon dioxide peaks, use OtherCorrections to remove these peaks.

? In OMNIC Help Topics find “water” in the Index and go to“H2O and CO2 correction.”

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Only those portions of the spectrum which are within the selectedregion (or displayed region if no region is selected) and within any ofthe regions you specified for the library using the Region Setup tabof the Library Setup dialog box will be included in the search. If thespectral range of the spectrum is broader than that of the libraryspectra, use the region tool to select the region of the spectrum thatcoincides with the library spectra before you start the search. Youcan also use the view finder to display the region to search. TheSearch command operates on the selected region, or on the displayedregion if a region is not selected.

? In OMNIC Help Topics find “spectral region” in the Index and go to“Region tool” or “View finder.”

How do I create a spectral library?

Use the Create Library button on the Library Names tab of LibraryManager to create a user library.

Once a library is created, you can add spectra to it with the Add ToLibrary button, with Add To Library in the Analyze menu, or bydragging the spectrum to the library’s book on the Library Namestab of Library Manager. You can use a search library you create justas you would a commercial library to identify unknown spectra. Youcan use a QC library to verify the composition of a sample. If youcreate a scrapbook library, you can find spectra in it by searching fortext (but not by spectral searching).

When you create a library, you determine the kinds of informationthat will be saved with it.

? In OMNIC Help Topics find “library” in the Index and go to“Creating a user library.”


How can I display a library spectrum in a spectral window?

Locate and select the spectrum in Library Manager and then click theAdd To Window button, or go to the Library Spectra tab of LibraryManager, display the desired spectrum on the tab and then double-click the spectrum.

? In OMNIC Help Topics find “library” in the Index and go to“Working with libraries.”

How can I find a compound in a commercial library?

Library Manager in the Analyze menu lets you search for thecompound name. After you select the library on the Library Namestab, use the features on the Search For Text tab to locate thespectrum. Type the text to search for in the Text In Selected Itembox, and then choose Search. The search results appear in the tablebased on the options you have set. To see information about a foundspectrum, double-click its row in the table.

? In OMNIC Help Topics find “library” in the Index and go to“Searching a library for text.”

You can use the extended search feature (available on the ExtendedSearch tab of the Library Setup dialog box) to find library spectra bysearching for text in any field included in the library. For example,some libraries have fields for molecular weight, boiling point ormanufacturer.

? In OMNIC Help Topics find “extended search” in the Index and goto “Using extended search.”

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What is the easiest way to collect sample spectra and add them toa spectral library?

Use the Collect Spectrum button on the Library Names tab ofLibrary Manager to collect a spectrum and add it to a user library.The software automatically sets the experiment parameters (forexample, Resolution) so that the spectrum will be compatible withthe selected library. This allows you to collect and add a compatiblespectrum in one step instead of three (using Experiment Setup to setthe parameters, Collect Sample to collect the spectrum and Add ToLibrary to add the spectrum to the library).

? In OMNIC Help Topics find “spectrum” in the Index and go to“Collecting a spectrum and adding it to a user library.”

What does the search expert do?

It determines the spectral regions to search, searches those regionsand then displays the specified number of library spectra that bestmatch the unknown spectrum, plus comments about the searchresults. For example, the search expert may tell you that the bestmatch is excellent but the second best match is also similar to theunknown. You will be able to display the list of matches to see theirmatch values and index numbers.


Opening, savingand deleting spectra

How do I open a stored spectrum?

Choose Open from the File menu, locate the spectrum or spectra youwant to open, select the filenames of the spectra and then chooseOK. You can hold down the Control key to select multiple files.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Opening spectra.”

How can I save my collected spectra automatically?

Choose Experiment Setup from the Collect menu and turn on SaveAutomatically on the Collect tab (Save Automatically is on bydefault). Specify a base name for naming the saved spectral data filesin the Base Name box. A sequential number will be appended to thebase name when the spectra are saved. If you want theinterferograms saved with the spectra, turn on Save Interferograms.Individual spectra are saved with the extension .SPA.


? In OMNIC Help Topics find “saving, spectra” in the Index and go to“File handling.”

Where should I save my spectra?

You have several options for saving spectra; you may choose to usemore than one.

For a permanent record of the spectrum and any other informationyou want to record, use a report notebook.

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? In OMNIC Help Topics find “report notebook” in the Index and goto “Adding a report to a notebook.”

You can also place spectra in descriptively named user libraries thatyou create. Keeping spectra in libraries allows you to find them bysearching for text contained in the information saved with thespectra.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Adding a spectrum to a user library.”

Note When you add a spectrum to user library whose resolution is lower,the spectrum is deresolved. For this reason it may be better in somecases to save your sample spectra as files on the hard disk andconsider the copies of them added to a user library to be forsearching purposes only. ▲

We recommend that you create descriptively named folders(directories) on your hard disk for different categories of spectra. Forexample, you could have a folder for each project you are workingon, for each of your clients, for each laboratory application, or foreach sample type. See your Windows documentation for informationon creating directories. You can specify which folder to use whenyou use Save or Save As in the File menu to save spectra. This willmake it easier to find a spectrum in a particular category when youuse Open in the File menu to open a spectrum.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Saving spectra using new filenames.”


How can I save several spectra in one file as a group?

Select the spectra and then choose Save Group from the File menu.To select more than one spectra, hold down the Control key andclick each spectrum you want to select with the selection tool, andthen release the Control key. Spectral groups are saved with theextension .SPG.

? In OMNIC Help Topics find “saving, spectra” in the Index and go to“Saving a group of spectra.”

How can I delete stored spectra?

Choose Delete Files from the File menu to display the Delete Filesdialog box. Locate and select the spectral data files (with theextension .SPA, or .SPG for spectral group files) you want to deleteand then choose OK.

? In OMNIC Help Topics find “spectra” in the Index and go to “Howto delete files.”

Can I delete an entry from a report notebook?

No. OMNIC’s report notebooks are similar to traditional laboratorynotebooks in that information you add to them becomes part of thepermanent record of your work.

You can delete an entire notebook, however, by deleting the entirenotebook file. Choose Delete Files from the File menu to display theDelete Files dialog box. Locate and select the directory containingthe notebook data files (with the extension .NBK). You will have toset the List Files Of Type box to All (*.*) to see .NBK files listed.Select the file you want to delete and then choose OK.

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Printing How can I specify a printer for printing information?

Use Printer Setup in the File menu. See your Windowsdocumentation for details on setting the printer parameters.

? In OMNIC Help Topics find “printer” in the Index and go to“Setting up the printer.”

How can I create and print reports of my work?

Use the commands in the Report menu. First use Template to select,edit or create a template for the report. Then use Preview/PrintReport to view the report as it will appear on paper. Click the Printbutton to print the report.

View Creating Reports (available through Learning OMNIC) tolearn about OMNIC’s report features.

? In OMNIC Help Topics find “template” in the Index and go to“Selecting, editing or creating a report template,” or find “report,previewing or printing” and go to “Previewing or printing a report.”

You can also use Add To Notebook to add the report to a reportnotebook. You can then print the report with the Print button whenyou view the notebook using View Notebook.

? In OMNIC Help Topics find “report” in the Index and go to “Addinga report to a notebook.”


How can I preview spectra or other information before printing?

Use Preview/Print Report in the Report menu to view a report as itwould appear on paper. The report is displayed using the currentreport template; that is, the template you have specified withTemplate or the template you are viewing and working with. If thereport is displayed as you want it to appear on paper, you can print itby using the Print button.

? In OMNIC Help Topics find “template” in the Index and go to“Selecting, editing or creating a report template,” or find “report,previewing or printing” and go to “Previewing or printing a report.”

Displaying spectra How can I select more than one spectrum at a time?

After selecting the first spectrum by clicking it, hold down theControl key while you click each additional spectrum. You can alsochoose Select All from the Edit menu to select all the spectra in thewindow that are not hidden.

? In OMNIC Help Topics find “spectra” in the Index and go to“Selection tool” or “Selecting all the spectra in a spectral window.”

How can I specify colors for displaying spectra?

Choose Options from the Edit menu, click the View tab and thenchoose Colors. In the Colors dialog box click the color next to thespectrum number for which you want to specify the color and thenclick the desired color in the color array. To specify the color forselected spectra, click the color next to Selected Spectrum and thenclick a color. Typically red is the color reserved for displayingselected spectra.

? In OMNIC Help Topics find “spectra” in the Index and go to“Specifying colors for spectra and other features.”

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You can also specify colors for displaying spectra in a particularspectral window. Start by selecting the spectra for which you want tospecify a color, and then choose Display Setup from the View menu.Click the desired color in the color array and then choose OK. Whenthe spectra are no longer selected, such as after you select a differentspectrum, they will be displayed in the color you clicked.

? In OMNIC Help Topics find “spectra” in the Index and go to“Selecting a color for the currently selected spectra.”

What is the difference between the Display Setup parametersand the Window options?

The parameters in the Display Setup dialog box affect the currentlyactive spectral window only. The options in the Window options (inthe Options dialog box) affect all the new spectral windows that youcreate. After you create a new spectral window, you can change theway spectra are displayed in it by using Display Setup.

? In OMNIC Help Topics find “display parameters” in the Index andgo to “Setting the display parameters,” or find “Window options”and go to “Window options.”

What can I do with the “Scale” commands in the View menu?

By using the appropriate command, you can display spectra so thatthey are easier to see or compare.

Full Scale displays the spectra so that they perfectly fit their panesvertically. Automatic Full Scale does this automatically when youchange the display with the view finder or selection tool. The Y-axisdisplayed corresponds to the selected spectrum.

Common Scale displays all the spectra so that they are not cut off atthe top or bottom and use the same Y scale. This allows you tocompare the band intensities of different spectra.


Match Scale changes the Y scale of the spectra to be the same as thatof the selected spectrum. (The selected spectrum’s scale is notchanged.) This allows you to compare the band intensities ofdifferent spectra.

Offset Scale shifts the spectra vertically so that they overlap less,making them easier to see.

When you use these commands, keep in mind that the current Y-axisis always accurate for the currently selected spectrum but may notapply to other spectra in the window.


For information on Full Scale or Automatic Full Scale, find“spectra” and go to “Displaying spectra full scale” or“Displaying spectra full scale automatically.”

For information on Common Scale, find “spectra” and go to“Displaying spectra using the same Y-axis.”

For information on Match Scale, find “spectra” and go to“Matching the Y scale of a spectrum.”

For information on Offset Scale, find “spectra” and go to“Displaying spectra vertically offset.”

How can I zoom in on an area of a spectrum?

Draw a box around the area using the selection tool and then clickinside the box.

You can also click the top half of the Expand/Contract button at theleft end of the view finder or drag the regions markers in the viewfinder to display a smaller spectral region.

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In addition you can use the Roll/Zoom window available in the Viewmenu (or click the Roll/Zoom Window button in the toolbar ifdisplayed) to expand an area.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Selection tool,” “View finder” or “Rolling and zooming spectra.”

How can I move a spectrum up or down in its pane to see itbetter?

Use the selection tool to drag the spectrum up or down.

You can also use the Roll/Zoom window available in the View menuto move a spectrum up or down.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Selection tool” or “Rolling and zooming spectra.”

How can I move a spectrum into another spectral window?

Use the selection tool to drag the spectrum from one spectralwindow to another. A copy of the spectrum appears in the secondwindow, and the original spectrum remains in the first window. Youcan also copy or cut the spectrum using Copy or Cut in the Editmenu and then paste it into another spectral window using Paste.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Selection tool,” or find “pasting, spectrum” and go to “Pastingitems.”

How can I move a stacked spectrum into another pane?

Use the selection tool to drag the spectrum from one pane intoanother.


? In OMNIC Help Topics find “spectrum” in the Index and go to“Selection tool.”

How can I find the X and Y values of a point in a spectrum?

Use the spectral cursor tool to click the point. The values aredisplayed in the readout above the palette.

? In OMNIC Help Topics find “X and Y values” in the Index and goto “Spectral cursor tool.”

How can I find the height of a peak?

Use the peak height tool to click the top of the peak. Then drag thebaseline handles to adjust the baseline used for the measurement.The corrected (measured above the baseline) and uncorrected heightvalues appear in the readout above the palette.

? In OMNIC Help Topics find “peak” in the Index and go to “Peakheight tool.”

How can I find the area of a peak?

Use the peak area tool to drag across the peak. Then drag thebaseline handles to adjust the baseline used for the measurement.The corrected (measured above the baseline) and uncorrected areavalues appear in the readout above the palette.

? In OMNIC Help Topics find “area” in the Index and go to “Peakarea tool.”

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Correcting spectra Should I correct the baseline of my spectrum?

If a baseline is sloped or curved or significantly above zeroabsorbance (or below 100% transmittance), a likely cause is how thesample was prepared. By correcting the baseline, you can oftenavoid having to prepare the sample again and collect a newspectrum.

Correcting a baseline will give you better results when you searchthe spectrum against a library, subtract the spectrum from anotherspectrum, find peaks in the spectrum or quantify components in thespectrum.

Collecting a Spectrum (available through Learning OMNIC)...“Common Problems with IR Spectra”

? In OMNIC Help Topics find “baseline” in the Index and go to“Correcting a baseline manually.”


Subtracting,adding, multiplying

and dividing spectra

How can I subtract a spectrum from another spectrum?

Use Subtract in the Process menu whenever you want to subtract onespectrum from another. Subtract is commonly used to removespectral features of solvent residues or pure components from thespectrum of a mixture of compounds.

Select the spectrum from which you want to subtract spectralfeatures; this is the sample spectrum. Then hold down the Controlkey and select the spectrum with the features you want to subtractfrom the sample spectrum; this is the reference spectrum.

Note Subtract is available only when two spectra are selected. ▲

Choose Subtract from the Process menu. The difference spectrum isdisplayed full scale in the bottom pane. This spectrum is the result ofsubtracting the reference spectrum from the sample spectrum usingthe subtraction factor shown to the left of the result. If you are notsatisfied with the subtraction result, you can change the subtractionfactor.

? In OMNIC Help Topics find “spectrum” in the Index and go to“Subtracting spectra.”

What should I use subtraction for?

Subtract is commonly used to remove spectral features of solventresidues or pure components from the spectrum of a mixture ofcompounds. When you use Subtract, the software calculates datapoint by data point the difference between the two.

Spectral subtraction is useful in a variety of situations. Here are someexamples:

• Eliminating solvent peaks in a spectrum of a sample that isdissolved in a solvent.

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• Separating components from a sample that is a mixture of two ormore components.

• Identifying an unknown contaminant by subtracting out theknown sample material.

• Ensuring quality by subtracting an original batch samplespectrum from a spectrum from the next batch.

What other mathematical operations can I perform on myspectra?

You can manipulate spectra using any of the common math operations.Use Spectral Math in the Process menu to perform these operations onone or two selected spectra. You specify the operations to perform bytyping a sequence of mathematical symbols and numbers. Thesoftware performs the operations on the Y values of the data points inthe spectrum or spectra and then displays the result spectrum.

When you choose the command, the Spectral Math window appearsallowing you to type the desired operations in the Operation text box.You can also select one of the example operations provided in theOperation drop-down list box.

View Using Spectral Math (available through Learning OMNIC).

? In OMNIC Help Topics find “spectrum” in the Index and go to“Performing arithmetic operations on spectra.”


Customizing OMNIC How can I customize my OMNIC software?

You can use Options in the Edit menu to set options that determinehow the software operates. You can also customize the menus andthe toolbar using Edit Menu and Edit Toolbar in the Edit menu. UseSave Configuration As in the File menu to save your customizedsettings in a configuration file. You can then open the file later toreset OMNIC to your preferences in one step.



Find “options” and go to “Customizing OMNIC by settingoptions.”

Find “menu” and go to “Customizing a menu.”

Find “toolbar” and go to “Customizing a toolbar.”

Find “configuration” and go to “Saving a configuration.”

Find “configuration” and go to “Opening a configuration.”

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Other questions How can I find and label peaks in spectra?

Use Find Peaks in the Analyze menu to find and label peaks above aspecified threshold.

You can also use the annotation tool to label individual peaks.

? In OMNIC Help Topics find “peaks” in the Index and go to “Findingpeaks above a specified height,” or find “label” and go to“Annotation tool.”

How can I close a task window (such as the Find Peaks window)?

Click the Close button (if available) in the upper-right corner of thewindow. You can also double-click the button at the left end of thewindow’s title bar (if the window is not maximized) or the button atthe left end of the menu bar (if the window is maximized).

? In OMNIC Help Topics find “task window” in the Index and go to“Task windows.”

How can I select a spectral region for an operation?

Use the region tool to drag across the region in the pane.

? In OMNIC Help Topics find “spectral region” in the Index and go to“Region tool.”


How can I display information about how a spectrum wascollected and processed?

Select the spectrum and then click the Information button to the leftof the title box. You can also double-click the spectrum’s title in thetitle box.

? In OMNIC Help Topics find “collection and processing information”in the Index and go to “Collection and processing information.”

If you want this kind of information displayed in a spectrum’s pane,choose Display Setup from the View menu, turn on SamplingInformation and then specify the types of information you wantdisplayed by turning on options in the Sampling Information box.

? In OMNIC Help Topics find “displaying, sampling information” inthe Index and go to “Displaying sampling information.”

How can I copy a spectrum and paste it into a text document?

Select the spectrum and choose Copy from the Edit menu. Thisplaces the spectrum on the Clipboard in the form of a Windowsmetafile (this is the file format with the most flexibility for pastinginto other programs). You can then paste the spectrum into adocument by using a word processing program.

? In OMNIC Help Topics find “copying, spectrum” in the Index andgo to “Copying items.”

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How can I get on-line Help while using the software?

The OMNIC on-line Help system lets you quickly find answers toyour questions about using the software. There are several ways toenter the Help system:

• To see information about a particular feature in OMNIC, clickthe feature using the right mouse button. A brief description ofthe feature appears, and in most cases one or more buttons thatyou can click to display more detailed information. Click theDiscussion button to display a complete discussion of the feature(or the dialog box or window that contains the feature). Click theHow To button to display a step-by-step procedure for using thefeature (or the dialog box or window that contains the feature).

• You can press the F1 function key at any time to see a discussiontopic for the currently displayed or selected feature, dialog box orwindow.

• If a dialog box or window contains a Help button, click it to seeinformation about the dialog box or window (or the commandthat displayed it).

• To see the Contents of the OMNIC Help system, choose OMNICHelp Topics from the Help menu.


Quick Answers to Your Questions AboutUsing the Spectrometer

This chapter answers some common questions about using yourspectrometer. Each answer is followed by a reference telling youwhere to go for more information.

Do I need to use an energy screen with my detector?

If you are using a highly sensitive detector such as a PbSe,Si, MCT-A or InSb detector and your experiment deals withinformation from a broad range of frequencies, use an energy screento prevent the detector from becoming saturated or producing adistorted signal.

Spectrometer Help Topics...“Installing an energy screen” in “Setting up experiments”

When do I need to open the spectrometer cover?

You need to open the spectrometer cover to change sources. Also,you need to open the cover if you are installing a spectrometercomponent such as a laser.

Spectrometer Help Topics...“Opening the main cover” in “Installing optional hardware”

Warning Do not operate the spectrometer with the main cover open. The coverprotects you from exposure to laser light and live electricalconnections. If you must open the main cover for maintenance orservice reasons, always turn the spectrometer power off first. ▲

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When should I align the spectrometer?

Align the spectrometer after you install a new beamsplitter, replacethe laser or move the spectrometer. It is also a good idea to align thespectrometer if the signal intensity has dropped significantly from itsusual level. For best performance align the spectrometer at least oncea week (once a day if you are performing step scan or other advancedexperiments).

? In OMNIC Help Topics find “aligning, spectrometer” in the Indexand go to “Aligning the spectrometer.”

Does my detector need to be cooled with liquid nitrogen?

Detectors that have a dewar need to be cooled. Dewar detectors arefairly large metal cylinders with a hole in the top. These includeMCT and InSb detectors. To determine if your detector requirescooling, open the detector compartment cover and see if the detectorhas a dewar.

If during a work session you find that the signal intensity from yourcooled detector is decreasing, it may need to be refilled with liquidnitrogen.

Spectrometer Help Topics...“Cooling a detector” in “Setting up experiments”

When should I change the desiccant (in sealed and desiccatedspectrometers only)?

If your spectrometer is in use, check the performance of thedesiccant by using the Check Desiccant button on the Diagnostic tabof the Experiment Setup dialog box. If the check indicates that thedesiccant is no longer effective, replace it.


Spectrometer Help Topics...“Checking and changing desiccant” in “Maintaining yourspectrometer”

If your spectrometer is in storage, check the round, blue indicator onthe desiccant holder under the beamsplitter compartment covermonthly. Change the desiccant if the indicator has turned pink.

See the replacement parts lists in “Ordering Parts” in SpectrometerHelp Topics to find the part number for desiccant bags. Thedesiccant holder under the beamsplitter compartment cover holdsone bag.

Which source should I use?

Use the source that is appropriate for the spectral range of yourexperiment (determined by the ranges of the beamsplitter anddetector). Nicolet offers a mid-IR to far-IR source (Ever-Glo) and anear-IR source (white light).

? In OMNIC Help Topics find “source” in the Index and go to“Specifying the source type.”

“Spectrometer Basics” chapter...“Selecting the right beamsplitter and detector” in “Usingbeamsplitters and detectors”

Should I turn off the spectrometer when I’m not using it?

We recommend that you leave the spectrometer on. This improvesthe thermal stability of the system and gives you more consistentresults when you collect spectra.

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How can I diagnose problems with the spectrometer?

The performance of the spectrometer is monitored while you collectspectra. If a problem occurs, a troubleshooting message appears.

See the “Troubleshooting” book in Spectrometer Help Topics forinstructions on diagnosing spectrometer problems and ordering andreplacing parts.

Note If you want to view the on-line videos to help you in troubleshootinga problem, put the Spectrometers Tutorials CD in the computer. ▲

You can also make a more thorough check on a spectrometercomponent by choosing Advanced Diagnostics from the Collectmenu. This starts the Bench Diagnostics program, which providesinformation on the status of the component as well astroubleshooting information, replacement procedures andinformation on ordering replacement parts.

“Diagnostics” chapter

? In OMNIC Help Topics find “diagnostics” in the Index and go to“Checking bench components.”

How do I replace parts in the spectrometer?

Spectrometer Help Topics...“Replacing parts”


Maintenance and Service

This chapter describes maintenance and service routines that you canperform on the spectrometer. We define maintenance as anoccasional procedure you perform to keep the spectrometer runningefficiently. We define service as a procedure to replace a failing partin the spectrometer.

Warning Perform only those procedures described in this chapter. If there areother problems, contact Nicolet at one of the numbers below.Outside the U.S.A. call your local sales or service representative.Telephone numbers for all Nicolet Customer Support offices areprovided with your system.

• Telephone (U.S.A.): 1-800-NICOLET (1-800-642-6538)• Fax: 1-608-273-5045• World Wide Web: http://www.nicolet.com• E-mail: [email protected] ▲

See the “Troubleshooting” book in Spectrometer Help Topics forinstructions on diagnosing spectrometer problems and ordering andreplacing parts.

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Aligning thespectrometer

and accessories

This section describes how to use the OMNIC software to align thespectrometer and accessories.

View “Maintaining your spectrometer” in Spectrometer Help Topicsfor instructions for other common maintenance procedures, such aschanging desiccant, cleaning the purge filter and cleaning the outsideof the spectrometer.

Aligning the spectrometer To ensure optimum system performance (high signal intensity, lownoise and good sensitivity), you should occasionally align thespectrometer using the OMNIC software.

Note If you have just turned on or moved the spectrometer, wait15 minutes (one hour for best results) before you align it so that itwill have time to stabilize. ▲

Follow these steps:

1. Remove any sample or accessory from the samplecompartment.

The beam path must be clear during alignment. Open the samplecompartment as briefly as possible to maintain a constant purge.

2. Choose Experiment Setup from the Collect menu.

The Experiment Setup dialog box appears.

3. Make sure Sample Compartment on the Bench tab is set toMain.

4. Set Gain on the Bench tab to 1.

Do not use Autogain.


An interferogram is shown in the live display. If you want toview a single-beam spectrum instead, turn on the Single Beamcheck box below the live display.

If you want to hear a tone whose pitch indicates the signalintensity, turn on the Tone check box below the live display. Thetone reaches its highest pitch when the signal is maximized.

5. To perform an alignment, click the Align button on theDiagnostic tab.

When you click the Align button, the system begins to optimizethe detector signal for maximum energy throughput. Alignmentshould take 2 to 4 minutes.

The live display of the detector signal changes as eachinterferogram is collected. The positive peak and negative peakintensities are shown next to Max and Min above the livedisplay. The interferogram location will be shown next toLocation, unless you turned on Single Beam.

6. When the alignment is finished, close the Experiment Setupdialog box.

Aligning an accessory You can also align accessories that mount inside a samplecompartment. First align the spectrometer without the accessoryinstalled, as described above. Then set Sample Compartment on theBench tab of the Experiment Setup dialog box according to theaccessory location. Set Gain to a value that gives a signal intensitythat is appropriate for the accessory. ATR and diffuse reflectionaccessories typically use a Gain setting of 2 or 4.

If you are not satisfied with the signal intensity after alignment, youcan manually align most accessories to maximize the signal. Forcomplete instructions, see the manual that came with the accessory.

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When you manually adjust an accessory, watch the largestinterferogram peak. The larger this peak, the better is the signalintensity.

Note The largest interferogram peak can be positive or negative. ▲

If you are unable to see the display, turn on Tone before adjustingthe accessory. The tone reaches its highest pitch when the signal ismaximized.


Servicing yourspectrometer

Three spectrometer components—the light source, the laser moduleand the main power supply—were designed so you can replace themyourself if they fail.

Note The diagnostics software will alert you to failing components. Forinstructions on diagnosing spectrometer problems, ordering parts andreplacing parts, choose Spectrometer Help Topics from the Helpmenu. ▲

If the source, laser module or power supply must be replaced, referto the replacement parts list made available when you chooseSpectrometer Help Topics from the Help menu. Call 1-800-NICOLET (1-800-642-6538) or 1-608-276-6373 to order thereplacement assembly. If you are outside the U.S.A., contact yourlocal Nicolet office. Telephone numbers for all Nicolet CustomerSupport offices are provided with your system.

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Diagnostics

This chapter explains how to use diagnostic software features to findand correct problems that occur when you use the system. We willcover...

• Checking the performance of spectrometer components.• Running the spectrometer performance test.• Performing advanced diagnostic tests.• Using remote diagnostics.

Checkingthe performanceof spectrometer

components

If your system is not performing properly, you can use theDiagnostic tab in the Experiment Setup dialog box to check theperformance of spectrometer components and determine the sourceof the problem.

Note OMNIC continuously monitors the operation of the spectrometerhardware and shows its status with the Bench Status indicator belowthe menu bar of the OMNIC window. See “The OMNIC window” inthe “Your First Experiment” chapter for more information. ▲

Follow these steps to run the spectrometer diagnostic tests:

1. Make sure the main sample compartment is empty.

Remove any samples and sampling accessories.

2. Choose Experiment Setup from the Collect menu.

The Experiment Setup dialog box appears.

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3. Click the Diagnostic tab.

The Diagnostic tab appears showing icons for the majorcomponents of the spectrometer with a live display of the signalfrom the detector.

4. To run the diagnostic tests for a component, click thatcomponent’s indicator icon.

A dialog box appears showing the status of the component. If theoperating values for the component are within proper limits, acheck mark appears in the Status column. If the value is outsidethe acceptable range, an X appears in the Status column.

When you are finished viewing the information, choose OK.


Running thespectrometer

performance test

You can use the performance test to track long-term spectrometerperformance. Run it after you have installed the system and thenweekly. Keep a record of the actual values obtained. When you runthe test, the software measures the response of the spectrometeroptics and atmospheric absorptions in the spectrometer and thencollects a “sample” spectrum with no sample in place. The result is a“100% line,” a display of system noise that appears as a generallyflat line at 100% transmittance.

Follow these steps:



2. Exit OMNIC.

This ensures that the diagnostics software will run correctly.

3. Start the diagnostics software.

To do this, click the Start button in Windows, point to Programs,point to the OMNIC E.S.P. folder and then choose BenchDiagnostics.

See “Performing advanced diagnostic tests” for moreinformation on running the diagnostics software.

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4. Click the Performance Tests button and follow theinstructions that appear on the screen.

Note If the noise readings are greater than normal or have changedsignificantly, call the Nicolet Customer Support Department forassistance. Outside the U.S.A., call your local service representative.Telephone numbers for all Nicolet Customer Support offices areprovided with your system. ▲

If special performance tests are available for your spectrometer, abutton labeled “Extended Tests” (or another appropriate name)will appear. Click this button and follow the instructions thatappear on the screen to perform the tests.

See “Running the remote diagnostics” for information aboutrunning performance tests for AM and PM step-scanexperiments, PEM experiments, rapid scan, and the expandedspectral range available with your spectrometer


Performing advanceddiagnostic tests

The diagnostics software provided with your system lets youperform advanced diagnostic tests on the main components of thespectrometer. You should run these tests if you have problems withyour spectrometer to determine the source of the problem. Thediagnostics provide information on the status of the component aswell as troubleshooting information, replacement procedures andinformation on ordering replacement parts.

Use the diagnostics software to:

• Run the spectrometer performance test.• Test specific components of your spectrometer.• Get information about replacement parts.• Check the spectrometer configuration.• Get troubleshooting tips.

Follow these steps to run the diagnostics:



2. Start the diagnostics software.

To do this, choose Advanced Diagnostics from the Collect menu.You can also click the Start button in Windows, point toPrograms, point to the OMNIC E.S.P. folder and then chooseBench Diagnostics. Some of the advanced features of thesoftware, including the performance test, are not available if yourun the diagnostics from OMNIC.

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3. Follow the directions that appear on the screen to run thediagnostic tests.

When you are finished viewing information in a window, youcan use the navigation buttons to return to earlier windows. Clickthis button to return to the previous window.

Click this button to return to the main Diagnostics window.

Exit the diagnostics software by clicking the Close button at thefar right end of the title bar.


Using remotediagnostics

The Nexus 870 is equipped with remote diagnostic capabilities. Thisincludes a data modem and remote control software that allowscontrol of your computer (and spectrometer) through the modemlink. To take advantage of the remote diagnostic capabilities, youmust have the modem connected to an analog telephone line.

Note We recommend that you dedicate a separate telephone line for datamodem calls. If you require assistance, Nicolet Customer Supportcan discuss the problem with you through the voice line whilerunning diagnostic tests on your system through the modem line. ▲

Remotediagnostic sessions

Follow these steps to start a remote diagnostic session:

1. Contact Nicolet and schedule a remote link.

Remote links are provided only within the system warrantyperiod or with an RSVP contract.

Note Steps 2, 3 and 4 must be completed before the scheduled remote link.The diagnostic session cannot begin until then. ▲

2. Exit the OMNIC software and close any open applications.

3. Start the remote control software.

Choose Start, point to Programs and then choose Carbon Copy 32in the Carbon Copy folder.

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4. Click the Wait For Call button.

You can also choose Wait For Call from the Connections menu.

5. Watch the screen while the remote session starts.

If you see any error messages, contact Nicolet Customer Supportby telephone for assistance.

Note Once the remote session starts, do not use your computer unless theservice engineer asks you to. When the service engineer is finished,the computer is returned to normal operating mode. ▲

Modem linespecifications

The data modem requires an analog phone line (an outside line inmost businesses). Many private branch exchange (PBX) phonesystems use digital phone lines that will not work with your datamodem. Ask your PBX administrator for a direct outside line or asampled analog trunk line.

Use the following guidelines to determine whether or not you havean analog phone line.

Rotary phone – All rotary phones are analog phones. If you hear adial tone when you plug a rotary phone into the phone wall jack, youhave an analog phone line and your data modem will work.

Push-button phone – If you have a push-button phone, check thebottom of the phone to see whether it has a ringer equivalencenumber (REN) or a load number (LN). All analog phones have anREN or an LN. If you hear a dial tone when you plug a push-buttonphone that has an REN or an LN into the wall jack, you have ananalog phone line and your data modem will work.


Wall jack specifications In the U.S.A., install an RJ-11 jack; in Canada, install a CA11Ajack. For other locations, contact your local Nicolet office for jackrequirements.

Running theremote diagnostics

The Bench Diagnostics program includes performance tests for AMand PM step-scan experiments, PEM experiments, rapid scan, SMMand the expanded spectral range available with your spectrometer.

Note If you plan to test the visible capabilities, make sure the quartzbeamsplitter, silicon detector and appropriate energy screen oroptical filter are installed in your spectrometer and selected (usingExperiment Setup) before you start the Bench Diagnostics. ▲

Follow these steps to test these capabilities:

1. Remove any samples or accessories from the samplecompartment.

2. Use Experiment Setup in the Collect menu to select thebeamsplitter you need for your tests.

If you are planning to run one of the visible tests, select thequartz beamsplitter.

3. Exit OMNIC.

4. Start the Bench Diagnostics.

Choose Start, point to Programs and then choose BenchDiagnostics in the OMNIC E.S.P. folder.

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5. Choose Performance Test.

6. Choose Advanced Tests.

7. Click the button labeled with the name of the test you wish torun.

Note Some tests are available only when the optional software is installedon your computer. ▲

About the individual tests The Bench Diagnostics program includes performance tests for AMand PM step-scan experiments, PEM experiments, rapid scan, SMMand the expanded spectral range available with your spectrometer.

Rapid scan When you choose Rapid Scan, the diagnostic checks the number ofscans per second at the highest linear scan velocity for yourspectrometer. The results are reported as number of scans per secondand indicate whether the bench passed or failed the test.

Visible Two visible spectral range tests are available. You must install andselect visible-light hardware before you use this test.

1. Install a quartz beamsplitter, silicon detector and blue filter.

Use the broad-band blue filter when testing the 23,000 to16,000 cm-1 capabilities.


Use the narrow-band blue filter when testing the 25,000 to23,000 cm-1 capabilities.

See “Installing optional hardware” in Spectrometer Help Topicsfor complete instructions for installing detectors, beamsplittersand filters.

2. Use OMNIC to select the visible light hardware.

AM step scan This test checks the amplitude modulation step-scan circuitry. Youmust install a cable and an energy screen before using this test.

1. Install the BNC-to-BNC cable.

Connect the cable between the Detector A and Internal Detectorconnectors on top of the spectrometer.

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2. Install energy screen B in the sample compartment.

In Spectrometer Help Topics view “Installing an energy screen”in the “Setting up experiments” book for instructions oninstalling energy screens.

You do not need to set any AM setup parameters before running thistest. Your parameters will be restored when the test is completed.

PEM This test checks the dual-channel circuitry. You must install cablesbefore using this test.

1. Install the BNC “T” connector.

Connect it to the Detector A connector on top of the spectrometeras shown in the illustration in the next step.


2. Install the BNC-to-BNC cables.

Connect one cable between the BNC “T” connector and theDetector B connector on top of the spectrometer. Connect theother cable between the BNC “T” connector and the InternalDetector connector.

You do not need to set any PEM setup parameters before runningthis test. You may need to reset the parameters before running yournext PEM experiment.

PM step scan This test checks the phase modulation step-scan circuitry in thespectrometer and reports the signal-to-noise ratio.

No cable connections are required, and you do not need to set anyPM setup parameters before running this test. Your parameters willbe restored when the test is completed.

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SMM This test is a simulation of an SMM (synchronous multiplemodulation) experiment. It verifies the basic operation of thespectrometer electronics.

This test requires cable connections.

Install the BNC-to-BNC cables.

Use one cable to connect the Internal Detector connector to theDetector B connector on top of the spectrometer. Use another cableto connect the Sync connector to the Laser connector on top of thespectrometer.

TRS This test checks the time-resolved step-scan circuitry in the opticalbench and is available only if your system is equipped with theoptional OMNIC SST with TRS Experiments software.


You do not need to set any TRS setup parameters before running thistest. Your parameters will be restored when the test is completed.The results will be reported as the signal-to-noise ratio and willindicate whether the spectrometer passed or failed.

You must install cables before selecting this test. You may also needa data acquisition card installed in your computer.

1. Install the BNC “T” connector.

Connect it to the Detector A connector on top of the spectrometeras shown in the illustration in the next step.

2. Install the BNC-to-BNC cables.

Connect one cable between the BNC “T” connector and theInternal Detector connector on top of the spectrometer.

Connect a second cable between the BNC “T” connector and thechannel 1 input on the data acquisition card (or the Detector Bconnector on top of the spectrometer, for internal TRS datacollection).

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Connect a third cable between the Trigger connector on top ofthe spectrometer to the trigger input (EXT) on the dataacquisition card.

To trigger input

Note Choose Yes when prompted for information about the backgroundsource. ▲

▲ Caution If you are not planning to run a TRS experiment, disconnect the dataacquisition card cables from the spectrometer when you finishrunning the TRS tests. Never leave the spectrometer connected to thedata acquisition card when you are not running TRS experiments ortests. It could affect your data. ▲


Troubleshooting Software Problems

The OMNIC software automatically and continuously checks thestatus of your system. If a problem is found, a message automaticallyappears giving you access to more information. This chapter listssome simple troubleshooting measures you can take to solvesoftware problems with OMNIC. If the action does not solve theproblem, call your Nicolet service office.

? In OMNIC Help Topics find “troubleshooting” in the Index and goto “Troubleshooting” for more information.

Problem Possible Cause Solution

After data collection,message says sampleand backgroundspectra have wrongresolution.

Resolution of currentbackground spectrum does notmatch resolution selected forsample spectrum collection.

Change Resolution to match backgroundand collect spectrum again. Use Resolutionparameter on Collect tab of ExperimentSetup dialog box.

Quantify command isdimmed.

No quantitative analysismethod is selected.

No spectrum is selected.

Quantitative analysis method isnot appropriate for selectedspectrum.

Select quantitative analysis method usingQuant Setup in Analyze menu.

Select single spectrum.

Select appropriate method for selectedspectrum.

You cannot addspectrum to userlibrary.

Resolution of spectrum islower (higher numerical value)than that of library.

Collect spectrum at same resolution aslibrary (first set Resolution on Bench tab ofExperiment Setup dialog box), and then addit to library.

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OMNIC needs to berestored after systemcrash, or messagestates that OMNICcannot start or will nolonger run.

There is not enough memory.

There is another systemproblem.

Make sure OMNIC has enough memory.Quit other programs to free memory forOMNIC.

Restart Windows.

Run SCANDISK utility included with yourWindows software.

Restart OMNIC. If OMNIC does not start,reinstall it.

Experiment providedwith OMNIC does notproduce good results.

Parameter settings inexperiment file have beenchanged so that experiment isno longer useful.

Restore experiment to its default settings:First open experiment using ExperimentSetup and save it using new filename if youdo not want to overwrite it. Then openexperiment in FACTORY directory whosefilename is same as original experiment andsave it in OMNIC\PARAM directory.

Desired experimentdoes not appear inExperiment drop-downlist box.

Experiment was installed withsoftware but has not yet beenopened.

If experiment was designed for Smartaccessory, install accessory; experiment willbe opened automatically and will appear inExperiment drop-down list box. Ifexperiment was not designed for Smartaccessory, open it using Experiment Setup;it will be added to list.

Libraries created withprevious version ofOMNIC are not listedin Library Setup dialogbox.

Libraries are not in one ofdirectories listed in dialog box(typically LIBS withinOMNIC directory).

Use Add Directory button on SearchLibraries tab to add directory.


Troubleshooting Hardware Problems

OMNIC continuously monitors the operation and status of yourspectrometer and informs you if a problem is found. The BenchStatus indicator below the menu bar shows the status of thespectrometer operation. When OMNIC performs a check and detectsa problem, the Bench Status indicator is displayed as a yellow circleor a red X along with an message alerting you to the problem.

If the indicator is a yellow circle, a cooled detector in the Nexus 870has become warm A message appears explaining the problem andallowing you to access information on correcting it.

If the indicator is a red X, the spectrometer has failed a diagnostictest and requires corrective action. A message appears explaining theproblem and allowing you to access information on correcting it.

This chapter lists some simple troubleshooting measures you cantake to solve problems with the spectrometer. The diagnosticssoftware is described in the “Diagnostics” chapter. If your actions donot solve the problem, call your Nicolet service office.

For more troubleshooting information see the “Troubleshooting”book in Spectrometer Help Topics.

Warning Always follow the safety precautions included in this manual and inyour Spectrometer Safety Guide when performing any of thefollowing troubleshooting procedures. ▲

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Status indicators do notlight when spectrometeris turned on.

Spectrometer is not plugged in. Make sure power cord is pluggedinto spectrometer and working walloutlet.

Check power LEDs on rear panel.All LEDs light when power supplyis working properly.

Power cable or power supply isdefective.

Call Nicolet to order replacementpart.

Data are not displayedduring collection.

Laser is not functioning. Hold business card or other smallpiece of white paper in beam path insample compartment to check forlaser light. Replace laser ifnecessary.

Data cable betweenspectrometer and computer isnot properly connected.

Turn spectrometer power off andcheck data cable connections.

Source status indicatoris off.

Source is burned out. Call Nicolet to order replacementsource. In Spectrometer Help Topicsview “Replacing your source” in“Replacing parts” to find partnumber, ordering and installationinstructions.

System does not scan. Laser is flickering. Hold business card or other smallpiece of white paper in beam path insample compartment to see if laserlight flickers. If it does, call Nicoletfor service.



There is frost on outsideof detector.

Insulating vacuum chambersurrounding dewar has begun toleak.

If you suspect your detector hasvacuum leak, view “Detector doesnot stay cooled” in“Troubleshooting” in SpectrometerHelp Topics.

Signal intensity is low,there are frequentmodulator scan restarts(verified by intermittentflashing of Scanindicator) andspectrometer alignmentfails.

Beamsplitter is fogged. Check laser signals by clicking laserindicator on Diagnostic tab inExperiment Setup dialog box. If yoususpect beamsplitter is fogged, callNicolet for service.

Baseline is not stable. Purge rate is too high. Lower purge rate until baseline isstable.

Center laser detector ismisaligned.

Use diagnostics software to checklaser levels for proper balance. Iflevels are out of tolerance, alignspectrometer using Align button onDiagnostic tab in Experiment Setupdialog box. If levels remain out oftolerance, call Nicolet for service.

Desiccant is expired. Replace desiccant.

Spectrometer cover wasrecently opened.

Allow spectrometer to purge for 3 to5 minutes after cover is closed.

Signal intensity is low inmid-IR range.

Source is glowing unevenly. Check to see if source element isglowing evenly. Order replacementsource if needed.

158 Nicolet


System scans but givesvery low signalintensity.

Spectrometer is out ofalignment.

Align spectrometer using Alignbutton on Diagnostic tab inExperiment Setup dialog box.

Detector and beamsplitter arenot compatible.

Make sure that selected detector andbeamsplitter are compatible. Changedetector or beamsplitter if necessary.

There is no interferogram. If Source status indicator is off, clicksource indicator on Diagnostic tab inExperiment Setup dialog box tocheck source current and voltage. IfSource indicator is on, checkinterferogram on Bench tab inExperiment Setup dialog box; ifinterferogram is not present, checkbeam path and detector.

You encounter problemswhen selecting externaldetectors on AEM, GCinterface or microscope.

Custom detector is selected onBench tab of Experiment Setupdialog box.

Detector cable is loose ataccessory connector (on rear ofspectrometer or on back wall ofsample compartment).

Set Detector to None on Bench tabof Experiment Setup dialog box.

Check and tighten cables.

Signal intensity is low,there are frequentmodulator scan restarts(verified by intermittentflashing of Scanindicator) andspectrometer alignmentfails.

Beamsplitter is fogged. Check laser signals by clicking laserindicator on Diagnostic tab inExperiment Setup dialog box,remove beamsplitter and checkbeamsplitter center window forfogging (check clear area located incenter of substrate). Replacebeamsplitter if necessary.



Laser status indicator isoff.

Beamsplitter compartmentcover is not fully closed.

Close beamsplitter compartmentcover.

Laser is burned out. Call Nicolet to order replacementlaser. View “Replacing the laser” in“Replacing parts” in SpectrometerHelp Topics to find part number andordering and installationinstructions.

Scan status indicatordoes not flash (system isnot scanning).

Spectrometer is out ofalignment.

Align spectrometer using Alignbutton on Diagnostic tab inExperiment Setup dialog box.

After 1 hour without datacollection activity,interferometer stops scanningand Scan light stays on. Thismode is normal.

Beamsplitter is not properlyseated.

Beamsplitter compartmentcover is ajar.

Electronic miscue has occurred.

Component has failed.

No action is required. Any datacollection activity will causeinterferometer to begin scanning.

Check beamsplitter and reposition itif necessary.

Close cover and tighten latch.

Press Reset button on rear panel.

Call Nicolet for service.

160 Nicolet


Error message appearswhen you try to scan.

Light source is not working. Check Source status indicator. Iflight is out, replace source.

Detector is not cooled. Check and cool detector.

Interferogram peak is notlocated at 1024 ±16 data pointson Bench tab in ExperimentSetup dialog box.

Align spectrometer. If interferogramis still not located correctly, callNicolet for service.

Beam path is blocked. Hold business card or other smallpiece of white paper in beam path insample compartment to check forlaser light. If no laser light is visible,beam path may be blocked. Removeobstruction.

Data cable betweenspectrometer and computer isnot properly connected.

Turn off spectrometer power andcheck data cable connections.

Detector and beamsplitter arenot compatible.

Change detector or beamsplitter.


Troubleshooting Applications Problems

If you have turned on OMNIC’s spectral quality checks feature, thesoftware automatically checks the status of collected interferograms,and background and sample spectra. When OMNIC performs acheck and detects a problem with data collection or spectra, theCollect Status indicator is displayed as a yellow circle or a red X.You can click the indicator (or click the View Collect Status buttonat the end of data collection) to see a summary of data collectionproblems encountered during the collection and other informationabout the collection.

This chapter lists some simple troubleshooting measures you cantake to solve data collection problems with the spectrometer. If theaction does not solve the problem, call your Nicolet service office.

? In OMNIC Help Topics find “troubleshooting” in the Index and goto “Troubleshooting” for more information.


Spectrum containsderivative-shaped peaks.

Sample in diffuse reflectionexperiment also has specularreflection component.

Correct spectrum by using OtherCorrections in Process menu. (SelectKramers-Kronig.)

Infrared beam was reflectedfrom (instead of penetrating)flat, shiny sample measuredusing specular reflectionaccessory.

Try using less reflective sample.

162 Nicolet


Spectrum contains totallyabsorbing peaks.

Sample in transmissionexperiment is too thick.

Use thinner sample.

Spectrum containscarbon dioxide peaks.

Spectrometer is not adequatelypurged.

Make sure you are using correct purgegas and that purge flow rate isadequate. Allow system three to fiveminutes to reestablish purge beforecollecting spectrum.

There are no peaks inspectrum.

There is no sample in infraredbeam path.

Check sample compartment oraccessory to make sure sample isproperly positioned in beam path.

Sampling cup in diffusereflection experiment is not inplace or is tilted.

Make sure cup is properly positionedin diffuse reflection accessory.

Infrared microscope is in itsviewing mode.

Put microscope in infrared mode andcollect spectrum again.

Sample film in attenuated totalreflection (ATR) experiment isbeing held against ATR crystalwith uneven pressure or haspoor contact with crystal.

Make sure sample is held evenly andhas good contact with crystal.

Spectrum contains waterpeaks.

Spectrometer is not adequatelypurged.

Make sure you are using correct purgegas and that purge flow rate isadequate. Allow system 3 to 5 minutesto reestablish purge before collectingspectrum.

Desiccant is expired. Check desiccant and replace it ifneeded.



Spectrum containsfringes or channeling.

Sample has parallel, highlyreflective sides that causeinfrared beam to bouncewithin sample when it isplaced perpendicular to beam.

Create new film using matte press.

Try roughening film surface slightlywith silicon carbide paper or othersuitable abrasive.

Rotate sample so that infrared beampasses through sample at Brewster’sangle. (Do not use this method if youare performing quantitative analysis ofsample.)

Baseline of spectrum isnot flat.

KBr pellet was made withcoarsely ground KBr powder,or KBr pellet was improperlypressed.

Be sure to press pellet properly.

Background spectrum for castfilm was collected with emptysample holder in infraredbeam.

Remove sample holder and collectbackground again.

Spectrometer is not properlyaligned, causing slopedbaseline.

Use Align button on Diagnostic tab inExperiment Setup dialog box to alignspectrometer.

Spectrometer has not been onlong enough to reach thermalequilibrium.

For best results allow spectrometer atleast one hour to stabilize after turningit on.

Spectrometer is not properlypurged.

Check system to make sure correctpurge gas is being used and that flowrate is correct.

164 Nicolet


Spectrum is too noisy. Detector is saturated. Add bandwidth-limiting filters orenergy screens to reduce signalstrength.

There were too few scans. Increase number of scans on Collecttab in Experiment Setup dialog box.

Resolution was too high. Reduce resolution on Collect tab inExperiment Setup dialog box.


Index

aabsorbance units, 37accessories, 85, 88

automated sample handling, 88descriptions, 88system, 92when to turn on, 13, 55

accessoryaligning, 133cabling, 93detector, 94installing, 88power, 94

Advanced Diagnostics, 130, 141AEM, 89aligning

accessory, 133spectrometer, 128, 132

AM step scan, 2, 74diagnostics, 147

annotation tool, 39, 124labeling peak using, 40pointer, 40

apertureeffect on resolution, 65effect on wavenumber accuracy, 65for collecting data in visible spectral range, 68for slow scan, 74resolution affected by, 67size for cooled detector, 65size for detector, 65

ATR accessory, 85, 86, 87ATR correction, 107Auxiliary 1 connector, 95Auxiliary 2 connector, 95Auxiliary connector, 94auxiliary experiment module, 89

bbackground spectrum

collected with sample holder in beam, 163collecting, 30defined, 22when to collect, 22

bandwidth-limiting filter, 64baseline

correcting, 106, 120not flat, 163not stable, 157sloped, 163

baseplateremoving, 88

beam pathblocked, 160

beamsplittercompatibility with detector, 60fogged, 157, 158installing, 128not compatible with detector, 158, 160not properly seated, 159spectral range, 61types, 59, 60

beamsplitter compartment cover, 159Bench Diagnostics, 130, 137, 145, 146

starting, 145Bench Status indicator, 21blanking totally absorbing bands, 106

ccable

not properly connected, 158, 160cabling

accessory, 93carbon dioxide peaks

removing, 107

166 Nicolet

channeling in spectrum, 163cleaning purge filter, 132closing window, 124Collect Sample, 30, 80Collect Sample window, 103Collect Status indicator, 34collecting

background spectrum, 30sample spectrum, 22, 25spectrum, 9, 19, 22, 25, 102

colorspectrum, 115

commercial libraryfinding compound in, 109

common scale, 116components

separating with subtraction, 122computer

when to turn on, 14, 56configuration

default, 25opening, 25saving, 123

connectorAuxiliary 1, 95Auxiliary 2, 95detector, 94Detector/Motors, 98pass-through, 93

connectorsfor custom accessories, 96pinouts, 97rear panel, 95sample compartment, 94

contaminantsidentifying with subtraction, 122

Continuµm, 89cooled detector

aperture size for, 65cooling detector, 15, 128copying

spectrum, 125correcting

baseline, 106, 120spectrum, 106

custom accessories, 96Custom baseplate, 89

ddata cable, 156data collection

parameters, 26default configuration, 25default experiment, 25deleting

report notebook, 113spectrum, 113

depth of penetration, 107desiccant

changing, 132checking, 12expired, 157, 162indicator, 12, 129when to change, 128

detectoraccessory, 94aperture size for, 65cable, 158compatibility with beamsplitter, 60connector, 94cooling, 15, 128custom, 158energy screen, 64, 67, 68, 127, 164external, 158frosted, 157linearity, 63not compatible with beamsplitter, 158, 160not cooled, 160optimizing performance of, 62photometric accuracy, 63saturated, 63, 64, 65, 164signal intensity, 133silicon, 68spectral range, 61types, 59, 60using filter to reduce energy reaching, 63

detector interface kit, 89Detector/Motors connector, 98


diagnostics, 137, 141, 143, 145, 146AM step scan, 147PEM, 148PM step scan, 149rapid scan, 146SMM, 150TRS, 150visible spectral range, 146

diffuse reflection accessory, 85, 87directory

library, 43, 154dispersion effects, 107Display Setup, 116distortion

in spectrum, 67documentation, 6

eenergy screen, 64, 67, 164

detectors typically used with, 64energy passed with, 64for collecting data in visible spectral range, 68resolution affected by, 67when to use, 127

error messageduring data collection, 160

Expand/Contract button, 117experiment

default, 25not listed, 154restoring, 154selecting, 17, 21, 25

Experiment drop-down list box, 17, 21, 25, 101Experiment Setup, 26extended search feature, 109extended spectral range, 69extension

notebook data file, 113spectral data file, 113

external beam, 88external detector, 158external source, 58

fF1 function key

for on-line Help, 7fiber optic accessory, 86filename

for saving spectrum, 36filter, 70

bandwidth-limiting, 64for collecting data in visible spectral range, 68installing in sample holder, 24reducing energy reaching detector using, 63

finding peaks, 124flammable gases, 10flowmeter, 10free spectral range, 69fringes

in spectrum, 163frost on detector, 157full scale, 116

ggain, 103

for collecting data in visible spectral range, 68gas cells, 89GC interface, 90Gemini, 90Getting Started tutorial, 2

hhard disk

saving spectra on, 112hardware requirements, 5Help, 6, 7, 126

OMNIC, 4SST, 76

iInformation button, 125infrared source, 58

168 Nicolet

InSb detectorcooling, 128

InspectIR, 89installing

accessory, 88beamsplitter, 128sample, 24, 32sample holder, 23

interferogram, 133location, 160not present, 158

interferogramssaving, 103saving automatically, 27

interferometerlong-stroke mode, 56, 159

kKBr pellet

improperly pressed, 163Kramers-Kronig, 161Kramers-Kronig correction, 107Kubelka-Munk units, 105

llabel

peak, 40labeling

peak, 124laser

burned out, 159flickering, 156not working, 156

laser frequency, 69Laser indicator, 14, 56library

adding spectrum to, 47, 110commercial, 109comparing sample spectrum with spectra in, 42creating, 7, 49, 108directory, 43, 154not listed, 154

saving spectra in, 112scrapbook, 108searching, 106spectrum cannot be added to, 153

Library Creation Wizard, 49Library Manager, 49library search

extended search feature, 109search expert, 110specifying spectral regions for, 108

library spectrumdisplaying, 109

liquid nitrogen for cooling detectors, 128live display, 133log (1/R) units, 105long-stroke mode, 56

mmaintenance, 131, 132manual conventions, 4matched scale, 117math operations

performing on spectra, 122MCT detector

cooling, 128memory insufficient, 154menu bar, 20menu names, 20microscope in viewing mode, 162microscopes, 89mirror velocity, 71moving

spectrum in pane, 118spectrum to another window, 118stacked spectrum, 118

nnear-IR sampling, 86noise, 64, 66nonaliased spectral range, 69number of scans

too low, 164


Nyquist theorem, 69offset scale, 117

oOMNIC

customizing, 123error message, 154Help, 4, 126starting, 16

OMNIC window, 20100% line, 139Open Configuration, 25opening

configuration, 25spectrometer cover, 127spectrum, 111

optical layout, 52, 53

ppalette, 39

selecting tool in, 39parameters

setting, 17pass-through connectors, 93, 96

pinouts, 97pasting

spectrum, 125peak

labeling, 40, 124peak area, 119peak height, 119peaks

carbon dioxide, 162derivative-shaped in spectrum, 161eliminating with subtraction, 121finding, 124noise, 164none in spectrum, 162totally absorbing in spectrum, 162water, 162

PEM, 2, 80diagnostics, 148

PEM kit, 90PEM step scan, 80% reflectance units, 105% transmittance units, 37performance test, 139, 141phase array, 79

calculating, 81correcting spectrum using, 80defined, 79saving, 84storing, 83viewing, 83

Phase Array Operations, 80phase correction

defined, 80photoacoustic accessory, 90photoacoustic units, 105photometric accuracy, 63, 65pinouts

connector, 97PM step scan, 2, 74

diagnostics, 149PM-IRRAS, 90power

accessory, 94Power indicator, 14, 56power line conditioner, 92power switch, 14pressure regulator, 10previewing report, 46, 114previewing spectrum before printing, 115printer

specifying, 114Printer Setup, 114printing report, 47pure air generator, 92purge

flow rate, 10, 11flow rate too high, 157gas, 10inadequate, 162, 163when to use, 10

purge filtercleaning, 132

purge gas generator, 92

170 Nicolet

qQC comparison

setting up, 42QC library, 42quality standards, 104Quantify, 153quantitative analysis, 63, 65, 153

rrapid scan, 71

diagnostics, 146Ratio Spectra, 77ratioing

spectra against common stored background, 77spectra using SST, 77two spectra, 78

rear panel, 54connectors, 95

regionselecting, 124

regionsspecifying for library search, 108

remote diagnostics, 143starting, 143telephone for, 143, 144wall jack for, 145

Remote Start accessory, 90replacing parts in spectrometer, 130report

creating, 45, 114previewing, 46, 114printing, 47

report notebookdeleting, 113saving spectra in, 111

report templatecreating, 46selecting, 45, 114

requirements of system, 5resolution, 153

affected by aperture, 65, 67affected by energy screen, 67and aperture, 65

effect of on signal-to-noise ratio, 66improving, 67incorrect, 153too high, 164

Roll/Zoom window, 118

ssafety, 2sample

installing, 24, 32not present, 162too thick, 162

sample compartmentconnectors, 94

sample filmin ATR experiment, 162

sample holderinstalling, 23installing sample or filter in, 24

sample shuttle, 91sample spacing, 69sample spectrum

adding to spectral library, 110adding to spectral window, 35collecting, 22, 25entering title for, 30

sample wheel, 88sampling accessories, 88sampling cup

missing or tilted, 162Sampling theorem, 69saturation, 164

detector, 63, 64, 65Save, 36Save As, 36saving

configuration, 123interferograms, 27, 103phase array, 84spectra, 27, 111spectra as group, 113spectra automatically, 111spectrum, 36


Scan indicator, 14, 56, 157, 158, 159scans

effect of number of on signal-to-noise ratio, 66number of, 33

scattering, 66scrapbook library, 49, 108sealed and desiccated system, 12, 129search

specifying spectral regions for, 108search expert, 110searching

preparing spectrum for, 106spectral library, 106

selectingexperiment, 17, 21, 25report template, 114spectral region, 124spectrum, 115

service, 131, 135signal intensity, 133

low, 158signal-to-noise ratio, 65, 66

increased by bandwidth-limiting filter, 64silicon detector, 68slow scan, 2, 73

filters for, 74parameters, 74

Smart Accessories, 85Smart Accessory, 21, 101Smart baseplate, 23, 89Smart Purge, 11, 31, 32Smart Purge Kit, 92SMM, 2

diagnostics, 150Snap-In sample compartment baseplates, 23software

preparing for data collection, 101requirements, 5troubleshooting, 153

source, 58burned out, 156external, 58glowing unevenly, 157not working, 160which to use, 129

Source indicator, 14, 56, 156spectra

saving as group, 113saving automatically, 27, 111subtracting, 121where to save, 111

spectral libraryadding spectrum to, 110creating, 7, 49, 108searching, 106

spectral quality checks, 29, 104spectral range, 69

detector-beamsplitter, 61visible, 68

spectral regionselecting, 124

spectral regionsfor library search, 108

spectral window, 20spectrometer

aligning, 132cover, 157, 159diagnostics, 130letting stabilize, 14maintaining, 132maintenance, 131not aligned, 159not purged, 162, 163optical layout, 52, 53out of alignment, 163parameters, 28performance test, 139purging, 10, 11rear panel, 54replacing parts in, 130service, 131servicing, 135status, 21troubleshooting, 155turning off, 55turning on, 13, 55when to align, 128when to open cover of, 127when to turn off, 129

172 Nicolet

spectrumbackground, 22baseline not flat, 163cannot be added to library, 153carbon dioxide peaks in, 162collecting, 19, 22, 25, 102collecting with SST, 76color, 115comparing with QC library spectra, 42copying and pasting, 125correcting, 106correcting baseline of, 120correcting with phase array, 80deleting, 113derivative-shaped peaks in, 161distorted, 67entering title for, 30fringes or channeling in, 163labeling, 40moving in pane, 118moving stacked, 118moving to another window, 118no peaks in, 162noise in, 164opening, 111preparing for search, 106preparing to collect, 9previewing before printing, 115ratioing against common stored background, 77ratioing with SST, 77saving, 36selecting, 115totally absorbing peaks in, 162units, 37, 102, 105water peaks in, 162zooming in on area of, 117

specular reflection, 91, 161SST, 75

collecting data using, 76ratioing spectra using, 77

startingBench Diagnostics, 145OMNIC, 16remote diagnostics, 143SST, 75

step scan, 2, 74, 76subtracting spectra, 121subtraction

when to use, 121system accessories, 92System Validation, 91

ttask window

closing, 124telephone for remote diagnostics, 143, 144telephone numbers, 3TGA interface, 91time-resolved step scan, 91title

entering for sample spectrum, 30tool

annotation, 39information, 39selecting, 39

toolbar, 21tools, 39totally absorbing bands

blanking, 106transmission accessory, 86, 91troubleshooting

applications, 161software, 153spectrometer, 155

TRS, 2diagnostics, 150

TRS step scan, 80turning off spectrometer, 55turning off system, 15, 56turning on computer, 14, 56turning on spectrometer, 13, 55tutorials, 6, 7

Getting Started, 2

uuninterruptable power supply, 92units used for spectrum, 37, 102, 105


User Example Library, 47user library

adding spectrum to, 47creating, 49saving spectra in, 112

user nameentering in OMNIC, 16

vvalidation wheel, 91VCD, 90velocity, 69, 71vibration

slow scan affected by, 74View Collect Status button, 34visible spectral range, 68

diagnostics, 146

wwall jack for remote diagnostics, 145water peaks, 162

removing, 107

wavenumber accuracy, 65window

closing, 124Window options, 116Windows metafile, 125wizard, 6, 7, 49

xX value

finding, 119

yY value

finding, 119Y-axis, 116

zZoom button, 46zooming in on spectrum, 117

Documents

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